bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasonographic imaging of calcifying fibrous tumor of cervical esophagus
Authors: Liu Yan , Lu Qiang , Wu Xiao-Li , Shen Guo-Ju , Luo Tao 
Published: July 2019

Abstract

Rationale:
Calcifying fibrous tumor (CFT) is a rare benign mesenchymal tumor characterized by cytologically benign fibroblasts that produce abundant collagen with scattered lymphocytes, plasma cells, and psammomatous or dystrophic calcifications.

Patient concerns:
A 37 years old women was initially diagnosed thyroid nodule in local hospital. She was referred to receive microwave ablation of the nodule in our hospital. The patient was in good health with occasional foreign body sensation in the neck. Routine laboratory examination was normal.

Diagnosis:
The lesion was suspected benign and originating from the esophagus rather than the thyroid gland by conventional ultrasound and contrast-enhanced ultrasound in our hospital and was finally proved to be CFT by pathology.

Interventions:
The lesion was surgically removed.

Outcomes:
The patient recovered well and was followed up for 2 years without recurrence.

Lessons:
Although imaging diagnosis of CFT is difficult, the findings of clear border, coarse calcification on conventional ultrasound and peripheral hypoenhancement without central enhancement on contrast-enhanced ultrasound (CEUS), together with real-time evaluation of the relationship between the tumor and esophagus help to distinguish CFT of cervical esophagus from other lesions in the neck.
The effect of fecal microbiota transplantation on Hepatic myelopathy
Authors: Sun Lin , Li Jun , Lan Li-Li , Li Xiao-An 
Published: July 2019

Abstract

Rationale:
Hepatic myelopathy (HM), also known as portal-systemic myelopathy, is a rare neurological complication that occurs in patients with chronic liver disease. There is no easy and feasible treatment, liver transplantation is the only accepted therapy that may be effective for patients at early stage at present. The pathogenesis of the disease is not clear yet, and the prognosis is poor. Here we describe a reversible HM after fecal microbiota transplantation.

Patient concerns:
In this report, a middle-aged female patient with hepatitis B cirrhosis, occurred HM after transjugular intrahepatic portosystemic shunt, a progressive spastic paraparesis in both legs were the main symptoms.

Diagnosis:
The patient was diagnosed with HM.

Interventions:
The patient received 3 times of fecal microbiota transplantations (FMT).

Outcomes:
The patient's muscle strength of both legs were increased at various degrees, the patient's condition improved from HM2 to HM1.

Lessons:
FMT may be another effective way to treat HM. It is cheaper, more operable, and simpler than the approved treatment and worthy of further research.
Chinese oral herbal paste for the treatment of stable chronic obstructive pulmonary disease
Authors: Zeng Yan , Li Yu , Wei Hua , Xiong Chan , Liao Li , Miao Ti-wei , Mao Bing , Fu Juan-juan 
Published: July 2019

Abstract

Background:
Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory disease with high morbidity and mortality placing heavy social and economic burden. As a kind of complementary therapy for the treatment of stable COPD, Chinese oral herbal paste has been widely used and studied. The study aims to evaluate the clinical efficacy and safety of herbal paste in the treatment of stable COPD, and to provide evidence for its clinical application.

Methods:
We will electronically search databases, including Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, EMBASE, PubMed, Chinese National Knowledge Infrastructure (CNKI), WANFANG Database, Chinese Scientific and Technological Periodical Database (VIP), and Chinese Biomedical Database (CBM), from respective inception to June 2019 to collect randomized controlled trials (RCTs) of Chinese oral herbal paste for the treatment of stable COPD. The websites of Chinese clinical trial registry and international clinical trial registry, the reference lists of the retrieved articles, conference proceedings, and gray literature will also be collected. The quality of life, symptom scores, and exacerbation frequency will be measured as primary outcomes. Secondary outcomes include scores of traditional Chinese medicine (TCM) syndrome, clinical effective rates according to criteria in TCM, changes in lung function, 6-minute walking distance, and safety analysis. The Cochrane bias risk assessment and the GRADE method will be used to assess the quality of the original studies included. Merging analysis of data will be performed using Rev Man 5.3 software.

Results:
The systematic review will provide an evidence on the clinical efficacy and safety of Chinese oral herbal paste for the treatment of stable COPD, and will be submitted for publication in a peer-reviewed journal.

Conclusion:
The study will confirm whether Chinese oral herbal paste is an effective and safe intervention for the prevention and treatment of stable COPD.
Association between endotoxemia and enterocyte injury and clinical course in patients with gram-positive septic shock
Authors: Sekino Motohiro , Funaoka Hiroyuki , Sato Shuntaro , Egashira Takashi , Inoue Haruka , Yano Rintaro , Matsumoto Sojiro , Ichinomiya Taiga , Higashijima Ushio , Matsumoto Shuhei , Hara Tetsuya 
Published: July 2019

Abstract
Endotoxemia often occurs in patients with gram-positive infections. The possible mechanism is thought to be bacterial translocation after enterocyte hypoperfusion injury. However, the association between endotoxemia and enterocyte injury among patients with gram-positive septic shock has never been assessed. The aim of this study was to evaluate the association between endotoxemia and enterocyte injury in gram-positive septic shock patients and to evaluate the association among endotoxemia, subsequent clinical course, and other related factors.
This was a posthoc analysis of a prospective observational study that evaluated the capability of intestinal fatty acid-binding protein (I-FABP), an indicator of enterocyte injury, to predict mortality. Among 57 patients in septic shock, those whose causative microorganisms were gram positive were included. The correlation between endotoxin activity (EA), which indicates endotoxemia, and I-FABP levels upon admission to the intensive care unit (ICU), the clinical course, and other related factors were evaluated.
A total of 21 patients were examined. One-third of the patients presented with high EA levels at the time of ICU admission. However, there was no significant correlation between EA and I-FABP levels (Spearman ρ = 0.002, P = .993). Additionally, high EA levels were not associated with abdominal complications after ICU admission or mortality. Similarly, high EA levels were not associated with severity scores, inotropic scores, or lactate levels upon ICU admission, which were previously reported to be factors related to high EA levels.
In this posthoc analysis, no correlation was observed between endotoxemia and enterocyte injury among patients in gram-positive septic shock. Additionally, high EA levels were not associated with the clinical course and reported factors related to endotoxemia. Although our results need to be validated in a large prospective cohort study, hypoperfusion enterocyte injury might not be a cause of endotoxemia in these patients. Thus, if there is no correlation between EA and I-FABP levels, other mechanisms that induce high EA levels among patients with gram-positive septic shock should be elucidated.
First-stage scapholunate fusion for the treatment of a chronic lunate dislocation
Authors: Huang Chao , You Di , Guo Wenlai , Qu Wenrui , Hu Yuchen , Li Rui , Zhu Zhe 
Published: July 2019

AbstractRationale:Lunate dislocation is a rare injury to the wrist caused by high-energy trauma, and poor prognosis is often associated with missed initial diagnosis. To date, there is no consensus regarding an effective treatment plan for such cases.Patient concerns:Here, we describe the case of a 36-year-old man who presented with lunate dislocation following a delay in diagnosis of over 7 weeks, and further illuminate its diagnosis and treatment.Diagnosis:The diagnosis of chronic lunate dislocation was rendered.Interventions:The patient was treated using reduction via the dorsal approach brachial plexus anesthesia. After the reduction, a headless compression screw fixation was performed for first-stage scapholunate fusion, and Kirschner wire fixation of the lunate-triquetrum-hamate was used to stabilize the distal and proximal carpal rows.Outcomes:The patient was followed up for 1 year and showed wrist function recovered well; radiographic examination showed no lunate dislocation and successful scapholunate bony fusion. A satisfactory outcome was achieved.Lessons:The case study presented here provide evidence that performing an effective first-stage scapholunate fusion is recommended to achieve better therapeutic outcomes for a chronic lunate dislocation. Furthermore, this approach led to a good long-term clinical outcome in our case.
Dilemma of Gonial Angle in Sex Determination
Authors: Bulut Ozgur , Freudenstein Nicolle , Hekimoglu Baki , Gurcan Safa 
Published: July 2019

Background and Aim
The determination of sex from human remains has a crucial role in forensic anthropology. It has been known that the mandible has several useful traits for sex determination. The gonial angle, which is one of them, has been evaluated by forensic practitioners to identify sexual dimorphism with morphologic and metrical analyses. However, there are opposing approaches on the sexual dimorphism of the gonial angle in the literature, which contradict each other. There are also some other studies asserting that it cannot be employed in sex determination. The purpose of this study is first to figure out the reason for this dilemma and then establish the significance of the gonial angle in sex determination in a white sample.

Methods
Computed tomography scans were obtained from 300 adults (150 males and 150 females), which were divided into 3 age groups (20–39, 40–59, 60–80 years). The gonial angle, which is formed by 2 lines: (1) between the most posterior point of the mandibular condyle and the gonion and (2) between the most inferior point of the mandibular symphysis and gonion, was measured on computed tomography scans. In order to observe differences among the 3 age groups, the collected data were analyzed using 1-way analysis of variance followed by a least significant difference post hoc test. Two-way analysis of variance was used to compare sex differences in each age group.

Discussion
It is suggested that the probable reason of this dilemma is the unsubtle samples of the researches. Categorizing the sample into age groups with statistically sufficient number makes the data more valuable in terms of examining the differences related to sexual dimorphism. This study also reported that males showed slightly smaller gonial angle values than those of females in all age groups. No statistically significant difference was observed in the gonial anthropometric values for middle age groups (20–39 and 40–59 years), whereas it shows statistically sexual dimorphism for senior adult group (60–80 years). However, the results revealed that the gonial angle is not a particularly good indicator to identify the sex from the cranium and should not be used as a sole criterion.
Tafenoquine: the new kid on the block
Authors: Chen Victor , Daily Johanna P. 
Published: July 2019

Purpose of review
This is a review of tafenoquine, a new antimalarial drug. Here we examine the recent literature supporting the use of tafenoquine and summarize the opportunities and challenges for its well tolerated use worldwide.

Recent findings
Tafenoquine was recently approved by the US Food and Drug Administration for the treatment of dormant liver stage (hypnozoite) in Plasmodium vivax and for malaria prophylaxis. Single-dose tafenoquine provides equivalent efficacy to 14 days of primaquine for radical cure in P. vivax, and it can be dosed weekly to prevent malaria. However, tafenoquine can only be used in patients with normal G6PD activity and is contraindicated in children and during pregnancy or in lactating mothers with infants of deficient or unknown G6PD status.

Summary
Tafenoquine's long half-life allows a single dose to achieve radical cure, and weekly dosing for chemoprophylaxis to provide an exciting therapeutic option for patient care and as a new weapon for malaria control/eradication programs. Global implementation of tafenoquine will require the development and validation of a robust, low-cost diagnostic to reliably identify G6PD-deficient individuals. In addition, studies on tafenoquine safety in children are needed.
WHO's new rabies recommendations: implications for high incidence countries
Authors: Pattanaik Amrita , Mani Reeta S. 
Published: July 2019

Purpose of review
Rabies is virtually always fatal; however, it is nearly 100% preventable with timely and appropriate prophylactic immunization. This review summarizes the recently revised WHO guidelines for rabies prophylaxis published in 2018, following a scientific review by a strategic advisory group of experts on immunization. The scientific basis for the major changes and its implications for countries with high disease burden are also discussed.

Recent findings
The key changes in the updated WHO 2018 guidelines for rabies prophylaxis include abbreviated vaccination regimens for pre and postexposure prophylaxis. These cost and dose-sparing regimens allow equitable sharing of vaccines, necessitate fewer clinic visits and thus can enhance patient compliance. The recommendations on rabies immunoglobulin administration permit prioritization and optimal use of this life-saving biologic, especially in areas with scarcity. However, there is a need for additional evidence to support the abridgment of some regimens and need for data on the safety and immunogenicity of these regimens in special groups such as infants and the immunocompromised.

Summary
National health authorities in high incidence countries need to develop consensus for effective implementation of simplified, cost-effective, and logistically feasible regimens for rabies prophylaxis, on the basis of the revised WHO guidelines.
Type 2 Diabetes Interacts With Alzheimer Disease Risk Factors to Predict Functional Decline
Authors: Thomas Kelsey R. , Bangen Katherine J. , Weigand Alexandra J. , Edmonds Emily C. , Sundermann Erin , Wong Christina G. , Eppig Joel , Werhane Madeleine L. , Delano-Wood Lisa , Bondi Mark W. 
Published: July 2019

Objective:The current study examined the interactive effect of type 2 diabetes and Alzheimer disease (AD) risk factors on the rate of functional decline in cognitively normal participants from the Alzheimer’s Disease Neuroimaging Initiative.Methods:Participants underwent annual assessments that included the Functional Activities Questionnaire, an informant-rated measure of everyday functioning. Multilevel modeling, controlling for demographic variables and ischemic risk, examined the interactive effects of diabetes status (diabetes, n=69; no diabetes, n=744) and AD risk factors in the prediction of 5-year longitudinal change in everyday functioning. One model was run for each AD risk factor, including: objectively-defined subtle cognitive decline (Obj-SCD), and genetic susceptibility [apolipoprotein E ε4 (APOE ε4) as well as cerebrospinal fluid β-amyloid (Aβ), total tau (tau), and hyperphosphorylated tau (p-tau).Results:The 3-way diabetes×AD risk factor×time interaction predicted increased rates of functional decline in models that examined Obj-SCD, APOE ε4, tau, and p-tau positivity, but not Aβ positivity.Conclusions:Participants with both diabetes and at least 1 AD risk factor (ie, Obj-SCD, APOE ε4, tau, and p-tau positivity) demonstrated faster functional decline compared with those without both risk factors (diabetes or AD). These findings have implications for early identification of, and perhaps earlier intervention for, diabetic individuals at risk for future functional difficulty.
P-hacking in clinical trials and how incentives shape the distribution of results across phases*
Authors: Adda Jérôme , Decker Christian , Ottaviani Marco 
Published: July 2019

AbstractClinical research should conform to high standards of ethical and scientific integrity, given that human lives are at stake. However, economic incentives can generate conflicts of interest for investigators, who may be inclined to withhold unfavorable results or even tamper with data in order to achieve desired outcomes. To shed light on the integrity of clinical trial results, this paper systematically analyzes the distribution of p-values of primary outcomes for phase II and phase III drug trials reported to theClinicalTrials.govregistry. First, we detect no bunching of results just above the classical 5% threshold for statistical significance. Second, a density discontinuity test reveals an upward jump at the 5% threshold for phase III results by small industry sponsors. Third, we document a larger fraction of significant results in phase III compared to phase II. Linking trials across phases, we find that early favorable results increase the likelihood of continuing into the next phase. Once we take into account this selective continuation, we can explain almost completely the excess of significant results in phase III for trials conducted by large industry sponsors. For small industry sponsors, instead, part of the excess remains unexplained.
High Resolution Tomographic Analysis of in vitro 3D Glioblastoma Tumor Model under Long-Term Drug Treatment
Authors: Ozturk Mehmet S. , Lee Vivian K. , Zou Hongyan , Friedel Roland H. , Dai Guohao , Intes Xavier 
Published: July 2019

AbstractGlioblastoma multiforme (GBM) is an extremely lethal type of brain tumor as it frequently develops therapeutic resistance over months of chemotherapy cycles. Hence, there is a critical need to provide relevant biological systems to guide the development of new potent personalized drugs but also efficient methodologies that enable personalized prediction of various therapeutic regimens for enhanced patient prognosis. Towards this goal, we report on the development of i) an appropriate in vitro model that mimics the 3D tumor microenvironment and ii) a companion imaging modality that enables to assess this in vitro model in its entirety. More precisely, we developed an integrated platform of bio-printing in vitro 3D GBM models and mesoscopic imaging to monitor tumor growth and invasion along with long-term drug treatment. The newly-developed in vitro 3D model contains tumor spheroids made of patient-derived glioma stem cells with a fluorescent reporter and vascular channels for drug perfusion. The imaging of these thick tissue constructs was performed using our second-Generation Mesoscopic Fluorescence Molecular Tomography (2GMFMT) imaging system which delivered 3D reconstruction of the fluidic channels and the GBM spheroids over the course of pre- and post-drug treatment (up to 70 days). The 2D measurements collected via 2GMFMT was comparable to existing imaging modalities, but 2GMFMT enabled non-sacrificial volumetric monitoring that provided a unique insgiht into the GBM spheroid growth and drug response. Overall, our integrated platform provides customizable in vitro model systems combined with an efficient long-term non-sacrificial imaging for the volumetric change of tumor mass, thus has a great potential in profoundly affecting the drug pipeline for a vast array of pathologies as well as for guiding personalized therapeutic regimen.
Deep learning regression model for antimicrobial peptide design
Authors: Witten Jacob , Witten Zack 
Published: July 2019

AbstractAntimicrobial peptides (AMPs) are naturally occurring or synthetic peptides that show promise for treating antibiotic-resistant pathogens. Machine learning techniques are increasingly used to identify naturally occurring AMPs, but there is a dearth of purely computational methods to design novel effective AMPs, which would speed AMP development. We collected a large database, Giant Repository of AMP Activities (GRAMPA), containing AMP sequences and associated MICs. We designed a convolutional neural network to perform combined classification and regression on peptide sequences to quantitatively predict AMP activity against Escherichia coli. Our predictions outperformed the state of the art at AMP classification and were also effective at regression, for which there were no publicly available comparisons. We then used our model to design novel AMPs and experimentally demonstrated activity of these AMPs against the pathogens E. coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Data, code, and neural network architecture and parameters are available at https://github.com/zswitten/Antimicrobial-Peptides.
Proliferation specific codon usage facilitates oncogene translation
Authors: Benisty Hannah , Weber Marc , Hernandez-Alias Xavier , Schaefer Martin H. , Serrano Luis 
Published: July 2019

SummaryTumors evolve under selection for gene mutations that give a growth advantage to the cancer cell. Intriguingly, some cancer genes are more often found mutated in tumors than their closely related family members. For example, KRAS mutations are more frequently observed in cancer in comparison to HRAS and NRAS. Here, we find that for RAS and six oncogene families, the most prevalent mutated members in cancer have a codon usage characteristic of genes involved in proliferation. The codon usage of KRAS is more adapted to be efficiently translated in proliferative cells than the codon usage of HRAS. We also show that the translation efficiency of KRAS varies between cell lines in a manner related to their tRNA expression. Altogether, our study demonstrates that a dynamic translation program contributes to shaping the expression profiles of oncogenes. We propose that codon bias related to cell proliferation contributes to the prevalence of mutations in certain members of oncogene families.
Genome-wide interologous interactome map (TeaGPIN) ofCamellia sinensis
Authors: Singh Gagandeep , Singh Vikram , Singh Vikram 
Published: July 2019

AbstractTea, prepared from the young leaves ofCamellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5,983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1,302 key proteins are reported in tea to havep-value < 0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.