PubTransformer

A site to transform Pubmed publications into these bibliographic reference formats: ADS, BibTeX, EndNote, ISI used by the Web of Knowledge, RIS, MEDLINE, Microsoft's Word 2007 XML.

- Top 30 Publications

Correction to: Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis.

Due to an unfortunate turn of events, the first name of the fifth author appeared incorrectly in the original publication and should have read Guangbing. The correct representation of the authors' names and their affiliation is listed here and should be treated as definitive.

Laparoscopic Surgery's 100 Most Influential Manuscripts: A Bibliometric Analysis.

Bibliometric analysis of the 100 most cited manuscripts in laparoscopic surgery.

Retrospective Analysis of Physician-based Surveys Published in OPRS.

To review physician-based clinical surveys published in Ophthalmic Plastic and Reconstructive Surgery.

A Large-Scale Analysis of Variance in Written Language.

The collection of very large text sources has revolutionized the study of natural language, leading to the development of several models of language learning and distributional semantics that extract sophisticated semantic representations of words based on the statistical redundancies contained within natural language (e.g., Griffiths, Steyvers, & Tenenbaum, ; Jones & Mewhort, ; Landauer & Dumais, ; Mikolov, Sutskever, Chen, Corrado, & Dean, ). The models treat knowledge as an interaction of processing mechanisms and the structure of language experience. But language experience is often treated agnostically. We report a distributional semantic analysis that shows written language in fiction books varies appreciably between books from the different genres, books from the same genre, and even books written by the same author. Given that current theories assume that word knowledge reflects an interaction between processing mechanisms and the language environment, the analysis shows the need for the field to engage in a more deliberate consideration and curation of the corpora used in computational studies of natural language processing.

Antibiotic therapy for preventing infections in people with acute stroke.

Stroke is the main cause of disability in high-income countries and ranks second as a cause of death worldwide. Infections occur frequently after stroke and may adversely affect outcome. Preventive antibiotic therapy in the acute phase of stroke may reduce the incidence of infections and improve outcome. In the previous version of this Cochrane Review, published in 2012, we found that antibiotics did reduce the risk of infection but did not reduce the number of dependent or deceased patients. However, included studies were small and heterogeneous. In 2015, two large clinical trials were published, warranting an update of this Review.

Rediscovering Don Swanson: the Past, Present and Future of Literature-Based Discovery.

The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for 2000, and as author of many seminal articles. In this informal essay, I will give my personal perspective on Don's contributions to science, and outline some current and future directions in literature-based discovery that are rooted in concepts that he developed.

A game of substrates: replication fork remodeling and its roles in genome stability and chemo-resistance.

During the hours that human cells spend in the DNA synthesis (S) phase of the cell cycle, they may encounter adversities such as DNA damage or shortage of nucleotides. Under these stresses, replication forks in DNA may experience slowing, stalling, and breakage. Fork remodeling mechanisms, which stabilize slow or stalled replication forks and ensure their ability to continue or resume replication, protect cells from genomic instability and carcinogenesis. Fork remodeling includes DNA strand exchanges that result in annealing of newly synthesized strands (fork reversal), controlled DNA resection, and cleavage of DNA strands. Defects in major tumor suppressor genes BRCA1 and BRCA2, and a subset of the Fanconi Anemia genes have been shown to result in deregulation in fork remodeling, and most prominently, loss of kilobases of nascent DNA from stalled replication forks. This phenomenon has recently gained spotlight as a potential marker and mediator of chemo-sensitivity in cancer cells and, conversely, its suppression - as a hallmark of acquired chemo-resistance. Moreover, nascent strand degradation at forks is now known to also trigger innate immune response to self-DNA. An increasingly sophisticated molecular description of these events now points at a combination of unbalanced fork reversal and end-resection as a root cause, yet also reveals the multi-layered complexity and heterogeneity of the underlying processes in normal and cancer cells.

Erratum: Author Correction: Successful amplification of DNA aboard the International Space Station.

[This corrects the article DOI: 10.1038/s41526-017-0033-9.].

Relationship between needling layers and needling sensations in acupuncture.

Based on the sancai (literally three talents referring to "earth", "human" and "heaven") and wuti (literally five organs referring to skin, muscle, vessel, tendon and bone, which correspond to five internal organs: lungs, spleen, heart, liver and kidney respectively) in Neijing (Internal Classic), as well as the tissue structure theory of modern anatomy, and in combination with the clinical practice of acupuncture by the author in the past over 30 years, it is proposed that four layers are divided in needling depth of acupuncture. The different needling sensations are induced at different layers. The first layer is the skin. When the needle is inserted into the skin, the main sensation is "pain". The second layer is the subcutaneous layer (superficial fascia). The needle tip at this layer generates a strong "swelling" sensation, which radiates along a certain direction. The third layer is the deep fascia and muscle layer. If the needle tip touches the deep fascia, there is a "heavy" feeling. If the needle tip goes into the muscle, an "acid" sensation will occur. The fourth layer is the periosteum and bone layer, which produces a strong sensation of "pain" when touched by the needle tip. In addition, each layer has blood vessels and nerve distribution. When the needle tip touches the blood vessels, a sense of "pain" happens. If the needle tip touches the nerve, there will be a sensation of numbness, which spreads along the direction of nerve conduction. On the contrary, through the patient's needling sensations, we can roughly know which layer and direction the needle tip goes. Better understanding of the relationship between the needling layers and needling sensations contributes to the further study of needling techniques, therapeutic effects of acupuncture and patient's sensations. It is significant for the regulations of needling sensations in patients.

Genetic Distances of Scallop (Chlamys farreri) Populations investigated by PCR Procedure.

The author performed PCR-based genetic platform to measure the hierarchical dendrogram of Euclidean genetic distances of Korean scallop populations (KSP), particularly for Chlamys farreri, which was further compared with those of the Chinese scallop populations (CSP), by employing the with specifically designed oligonucleotide primer sets. The scallop is economically and ecologically very important bivalves in South Korea. Relatively, individuals of KSP population were fairly distantly related to that of CSP population, as shown in the hierarchical dendrogram of Euclidean genetic distances. Comparatively, individuals of KSP population were fairly distantly related to that of CSP population. Thus analysis of genetic difference between scallop populations could provide important statistics for fishery and aquaculture. Overall the results showed specific and/or conserved genetic loci between scallop populations. Information on the genetic distance of the bivalve would be helpful to understand scallop expansion or conservation in the coastal regions of South Korea. Specific markers developed by the author will be useful for the analysis of scallop population genetics and distribution in coastal region.

Rare gastrointestinal stromal tumors (GIST): omentum and retroperitoneum.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms that arise in the gastrointestinal tract and rarely elsewhere in the abdomen. GISTs that develop outside the digestive tract are called extra-GISTs (EGISTs). The incidence of EGISTs is reported to be approximately 10% of all GISTs, and the median age is younger than that of conventional GISTs. EGISTs have similar histology and immunohistochemical features as conventional GISTs, with the majority of them in the omentum and mesentery. Most GISTs harbor a kinase-activating mutation in either KIT or PDGFRA. For EGISTs, the incidence of this type of mutation is 40-50%, which is somewhat lower than for conventional GISTs. EGISTs may have a worse prognosis compared with conventional GISTs with high mitotic indices, large size, and distant metastasis including lymph node involvement. In large abdominal tumors, the visceral origin is almost impossible to discern.

Predicting fatalities in serious idiosyncratic drug-induced liver injury-a matter of choosing the best Hy's law.

Surgical treatment of gastrointestinal stromal tumors of the stomach: current status and future perspective.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract, with the majority found in the stomach. Surgical resection of the primary gastric GISTs with complete resection margin has been the forefront of curative treatment. The indications for surgical resection are usually related to symptomatic gastric GISTs at presentation. Primary gastric GISTs resection performed conventionally through an open surgery can now be frequently achieved by minimal invasive surgery with similar oncological outcome. Surgeon's selection of the type of surgical techniques such as open, laparoscopic and endoscopic resections depends on the site, size and local invasion of gastric GISTs to the adjacent organ. Similarly those factors dictate the extent of gastric resections in the form of wedge, partial or total gastrectomy. All these inherent tumor factors (size and mitotic index), patient factors (older age, male) and surgical factors (incomplete resection margin, tumor rupture or spillage) play an important role in stratifying the malignant potential risk of primary gastric GISTs and their chances of recurrence. The understanding of gene mutation driving the growth of GISTs and the discovery of tyrosine kinase inhibitors (TKIs) has altered the surgical management of advanced and metastatic GISTs. Multi-modal therapy incorporating the surgical resection of GISTs and utilizing the molecular targeted therapy in the adjuvant, neoadjuvant and palliative settings can offer optimal personalized outcome and prolong patient's overall survival (OS).

Long-term results with percutaneous interspinous process devices in the treatment of neurogenic intermittent claudication.

Neurogenic intermittent claudication (NIC) is the main symptom of degenerative lumbar spinal stenosis. Percutaneous interspinous process decompression devices (IPDs) have been designed as an alternative therapy to conservative treatment and to open decompressive surgery for patients suffering from NIC. Initial short-term results were encouraging. We present the long-term results of a group of patients that we followed to provide insight on long-term outcomes and effectiveness of this technique compared to other decompression methods.

Single-Photon Nanoantennas.

Single-photon nanoantennas are broadband strongly scattering nanostructures placed in the near field of a single quantum emitter, with the goal to enhance the coupling between the emitter and far-field radiation channels. Recently, great strides have been made in the use of nanoantennas to realize fluorescence brightness enhancements, and Purcell enhancements, of several orders of magnitude. This perspective reviews the key figures of merit by which single-photon nanoantenna performance is quantified and the recent advances in measuring these metrics unambiguously. Next, this perspective discusses what the state of the art is in terms of fluoresent brightness enhancements, Purcell factors, and directivity control on the level of single photons. Finally, I discuss future challenges for single-photon nanoantennas.

The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering.

Synthetic Biology (SB) aims at the rational design and engineering of novel biological functions and systems. By facilitating the engineering of living organisms, SB promises to facilitate the development of many new applications for health, biomanufacturing, and the environment. Over the last decade, SB promoted the construction of libraries of components enabling the fine-tuning of genetic circuits expression and the development of novel genome engineering methodologies for many organisms of interest. SB thus opened new perspectives in the field of metabolic engineering, which was until then mainly limited to (over)producing naturally synthesized metabolic compounds. To engineer efficient cell factories, it is key to precisely reroute cellular resources from the central carbon metabolism (CCM) to the synthetic circuitry. This task is however difficult as there is still significant lack of knowledge regarding both the function of several metabolic components and the regulation of the CCM fluxes for many industrially important bacteria. Pyruvate is a pivotal metabolite at the heart of the CCM and a key precursor for the synthesis of several commodity compounds and fine chemicals. Numerous bacterial species can also use it as a carbon source when present in the environment but bacterial, pyruvate-specific uptake systems were to be discovered. This is an issue for metabolic engineering as one can imagine to make use of pyruvate transport systems to replenish synthetic metabolic pathways towards the synthesis of chemicals of interest. Here we describe a recent study (MBio 8(5): e00976-17), which identified and characterized a pyruvate transport system in the Gram-positive (G+ve) bacterium Bacillus subtilis, a well-established biotechnological workhorse for the production of enzymes, fine chemicals and antibiotics. This study also revealed that the activity of the two-component system (TCS) responsible for its induction is retro-inhibited by the level of pyruvate influx. Following up on the open question which is whether this retro-inhibition is a generic mechanism for TCSs, we will discuss the implications in metabolic engineering.

The Effect of Foeniculum Vulgare (Fennel) on Body Composition in Postmenopausal Women with Excess Weight: A Double-blind Randomized Placebo-controlled Trial.

The goal of this study was to evaluate the effect of fennel on body composition.

Overcoming barriers to intranasal corticosteroid use in patients with uncontrolled allergic rhinitis.

Patients suffering from allergic rhinitis often attempt to self-manage their symptoms and may seek advice from pharmacists about nonprescription product choices. Several drug classes, both prescription and over-the-counter (OTC), are available, including intranasal corticosteroids (INCSs); oral, intranasal, and ocular antihistamines; leukotriene antagonists; and topical and systemic decongestants, as well as immunotherapies. Selection of the optimal treatment approach depends on the temporal pattern, frequency, and severity of symptoms as well as the patient's age. Nasal congestion is typically the most bothersome symptom, although rhinorrhea, postnasal drip, and ocular symptoms are also problematic. Together, these symptoms may adversely impact the quality of life, work productivity, sleep quality, and the ability to perform daily activities, particularly when uncontrolled. Practice guidelines recognize that INCSs are the most effective medications for controlling allergic rhinitis symptoms, including nasal congestion. Available INCS products have comparable safety and efficacy profiles, but they differ in formulation characteristics and sensory attributes. Several barriers can impede the use of INCSs, including concerns about safety, misperceptions regarding the loss of response from frequent use, and undesirable sensations associated with intranasal administration. Given the increasing number of INCSs available OTC, pharmacists can help allay these concerns by discussing treatment expectations, recommending INCS products with favorable formulation characteristics, and reviewing proper use and technique for the administration of the selected product. These steps can help to foster a collaborative relationship between the patient and the pharmacist in the treatment of allergic rhinitis.

The impact of perioperative blood transfusion on survival outcomes in radical cystectomy patients.

The landscape of genetics and biomarkers in bladder cancer.

Imaging of Abductor Tears: Stepwise Technique for Accurate Diagnosis.

This article presents the authors' technique for evaluation of possible abductor tears with magnetic resonance imaging (MRI). By using T2 fat-saturated coronal and axial slices of the hip and T1 coronal images of the pelvis, the authors show how to visualize all tears of the abductor tendons and signs of chronic abductor deficiency. After diagnosis has been made, signs that may help the surgeon determine if open or arthroscopic surgery would be best used are reviewed. Finally, the author reviews indications for a gluteus medius repair with concomitant gluteus maximus reconstruction.

Calligonum comosum and Fusarium sp. extracts as bio-mediator in silver nanoparticles formation: characterization, antioxidant and antibacterial capability.

In the current study, extracellular biosynthesis of silver nanoparticles (AgNPs) was carried out using aqueous extracts of green Calligonum comosum stem, besides Fusarium sp. Synthesized AgNPs were characterized using ultraviolet (UV)-Vis spectrophotometer, transmission electron microscopy (TEM) and zeta potential. Moreover, biosynthesized AgNPs were estimated for the scavenging ability on DPPH radical as well as tested for their antibacterial activity using well diffusion method against Gram-positive bacteria Staphylococcus aureus. On the other hand, DNA content from untreated and AgNPs treated bacterial cells was evaluated by (UV)-Vis spectrophotometer and agarose gel electrophoresis. Results revealed the formation of AgNPs, which was first detected by color change of the reaction mixture. The characteristic surface plasmon resonance absorption was detected at 450 and 410 nm for the plant and myco-synthesized AgNPs. Furthermore, TEM micrograph and zeta sizer showed formation of spherical particles with an average size of about 105.8 and 228.4 nm for plant and myco-synthesized AgNPs, respectively. Plant-synthesized AgNPs exhibited higher scavenging of DPPH radicals than that of the myco-synthesized one. For bactericidal action, plant-synthesized AgNPs showed higher inhibition zone compared with myco-synthesized one, which was negatively correlated with the nanoparticle size. Furthermore, low DNA concentration was detected for AgNPs treated bacteria, which might be a consequence of inactivation for DNA replication. Further experimental work is required to find out if there is any correlation between nanoparticles size and efficacy against bacteria.

The production of UL16-binding protein 1 targeted pigs using CRISPR technology.

Two sgRNAs were designed to target the region of exon 2 of the pULBP1 gene by microinjection. The co-injection of modified Cas9-D10A nickase with a pair of sgRNAs into the zygote's cytoplasm easily and efficiently generated biallelic modification of the pULBP1 gene in one step. Five out of nine F0 generation piglets showed insertions or deletions in the targeting site of the pULBP1 gene, indicating that pULBP1 mutation efficiency reached about 56% (5/9). Quantitative determination of pULBP1 showed approximately a 1.53-fold reduction in the amount of protein ULBP1 on the cell surface (ELISA). A human NK-cell cytotoxicity test leads to the conclusion that higher cell viability is observed for -/- ULBP1 (survival rate 85.36%) compared to +/+ ULBP1 (69.58%). ULBP1-KO pigs will provide a more progressive xenograft source for further research studies, especially those measuring the effects of abolishing the gene function in terms of the complexity of the immunological interactions.

Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae).

This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.

Transvenous Aneurysm Sac and Rupture Point Coil Embolization of Direct Carotid Cavernous Fistula after Pipeline Embolization.

A delayed aneurysm rupture after flow diverter therapy is a rare but serious complication. Due to the anatomical specificity, a delayed rupture of a carotid cavernous aneurysm may cause a direct carotid cavernous fistula (dCCF). We present a novel therapeutic approach for treatment of dCCF after flow diverter therapy using the Pipeline embolization device (PED). An 86-year-old woman suffered from dCCF after PED embolization. A microcatheter was advanced through the transvenous approach into the cavernous sinus (CS) and further inserted into the aneurysm sac via the rupture point. Coil embolization of both the aneurysm sac and a small part of the CS adjacent to the fistulous site could achieve not only the immediate aneurysm occlusion but also the rupture point obliteration with a small amount of coil mass in the CS.

Advanced dental implant placement techniques.

The availability of in office Cone Beam CT (CBCT) scanners, dental implant planning software, CAD CAM milling, and rapid printing technologies allow for the precise placement of dental implants and immediate prosthetic temporization. These technologies allow for flapless implant placement, or open flap bone reduction for "All on 4" techniques with improved preoperative planning and intraoperative performance. CBCT permits practitioners in an office setting with powerful diagnostic capabilities for the evaluation of bone quality and quantity, as well as dental and osseous pathology essential for better informed dental implant treatment. CBCT provides the convenience of in office imaging and decreased radiation exposure. Rapid printing technologies provide decreased time and high accuracy for bone model and surgical guide fabrication.

Compare the Intracranial Pressure Trend after the Decompressive Craniectomy between Massive Intracerebral Hemorrhagic and Major Ischemic Stroke Patients.

Massive intracerebral hemorrhage (ICH) and major infarction (MI) are devastating cerebral vascular diseases. Decompression craniectomy (DC) is a common treatment approach for these diseases and acceptable clinical results have been reported. Author experienced the postoperative intracranaial pressure (ICP) trend is somewhat different between the ICH and MI patients. In this study, we compare the ICP trend following DC and evaluate the clinical significance.

The role of biopsies and autopsies in the diagnosis of cognitive impairment, with emphasis on small vessel diseases: A critical appraisal enriched by personal experience.

Acquired and hereditary microangiopathies cause cerebral small vessel diseases (CSVD) that impair cognition. The most frequent is primary angiitis of the CNS (PACNS), whose diagnosis remains challenging, requiring a multidisciplinary approach. Secondary vasculitis, CADASIL, miscellaneous microangiopathies and lymphomas, also cause cognitive impairment. Despite the fact that the need for biopsy has decreased in the era of new neuroimaging methods, biopsies that include small leptomeningeal and parenchymal arterial vessels still remain the gold standard to diagnose PACNS and other CSVD, and to exclude mimics such as infections and malignancies. New approaches for pathological consequences relevant to vascular cognitive impairment such as silent brain lesions, microinfarcts, microbleeds and subtle loss of microstructural integrity, may be detected in autopsies. This article addresses the role of biopsies and autopsies for the diagnosis of cognitive impairment related to small vessel diseases or other inflammatory/ischemic processes, and presents a critical appraisal based on personal experience.

The physician as person framework: How human nature impacts empathy, depression, burnout, and the practice of medicine.

Troubling trends of depression, burnout, and declines in empathy have been demonstrated amongst residents. I argue that while interventions in medical education are helpful, a new perspective on the issue requires a more fundamental understanding of this problem. Rather than training physicians to act in certain ways, we must first recognize that physicians are first and foremost people. This core principle forms the basis of the framework that educators can use to help learners. Five areas of humanity with implications for physicians are discussed: 1) Physicians and patients share their humanity; 2) People are self-integrated in both personal and professional lives; 3) People are dynamic, thoughtful, and emotional; 4) People are finite; and 5) People are moral beings. Recognizing these can mitigate various factors contributing to current struggles. I also discuss practical implications of this framework to help residents flourish.

Early arriving males wait longer for a mate than later arrivals: the case of a migratory monogamous passerine bird species.

Individuals that arrive earlier on the breeding grounds may obtain many advantages but they also have to spend time waiting for a mate. I studied the waiting times of male red-breasted flycatchers Ficedula parva, a small, migratory, sexually dichromatic passerine bird species under natural conditions (Białowieża National Park, Poland) in relation to year, arrival time, age of male and morphological parameters. The length of waiting time was dependent on males' arrival time. The males which arrived later waited a shorter time for females than earlier arrivals. In some years older males spent more time waiting for mates than younger males, but in other years they waited for shorter times. A significant interaction between age of male and year was also observed. Despite the significantly earlier arrival of older males, the waiting time was not related to male age. The waiting time was also not related to body biometric parameters of the male. Despite waiting longer, early male red-breasted flycatchers have an advantage over later arrivals given this greater chance of mating.