bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of Gonioscopy-assisted Transluminal Trabeculotomy in Vitrectomized Patients With Secondary Glaucoma After Silicone Oil Removal
Authors: Aktas Zeynep , Ucgul Ahmet Y. , Ozdek Sengul , Boluk Ceyda E. 
Published: November 2020

Précis:
The present study demonstrates that surgical success rates of gonioscopy-assisted transluminal trabeculotomy (GATT) with a target intraocular pressure (IOP)≤21 mm Hg are 93.3% (for qualified success) and 26.7% (for complete success) in vitrectomized patients exhibiting secondary open-angle glaucoma (SOAG) after silicone oil (SO) removal, for an average follow-up of 37.5 months.

Purpose:
To report the long-term outcomes of GATT in vitrectomized patients exhibiting SOAG after SO removal.

Setting:
Retrospective case-series study.

Patient Population:
This retrospective case-series study enrolled vitrectomized patients who underwent uneventful GATT surgery between May 2014 and May 2019 at Gazi University Hospital for the treatment of medically uncontrolled SOAG after SO removal.

Main Outcome Measures:
At baseline and at each postoperative visit, a detailed ophthalmic examination consisting of slit-lamp biomicroscopy, indirect ophthalmoscopy, macular optical coherence tomography, and Goldmann applanation tonometry was performed in all patients. Baseline demographic and clinical characteristics, duration between pars plana vitrectomy and SO removal, duration between SO removal and onset of SOAG, follow-up time, need for antiglaucoma medication, visual acuity, and IOP measurements were noted. Surgical success was defined as an IOP≤21 and ≥6 mm Hg with (qualified success) and without (complete success) IOP-lowering medication.

Results:
A total of 15 patients had a history of pars plana vitrectomy with 1000 centistoke SO tamponade before the GATT surgery. GATT was performed in all patients with SOAG after SO removal. The mean age and follow-up of the patients were 53.6±11.8 years (range, 34 to 72 y) and 37.5±15.1 months (range, 12 to 61 mo), respectively. The average duration of SO tamponade in the vitreous cavity was 7.5±1.6 months (range, 5 to 10 mo). The average duration between the SO removal and the development of SOAG was 14.1±13.2 months (range, 2 to 46 mo). The mean IOP decreased from 31.0±4.1 mm Hg at baseline to 15.6±4.6 mm Hg at final visit. The mean final logMAR BCVA was 0.92±0.58 (range, 2 to 0.045). Qualified surgical success was achieved in 14 (93.3%) patients, whereas complete success was achieved in only 4 (26.7%) patients (P<0.001).

Conclusions:
GATT seems to be safe and successful procedure for controlling IOP in patients exhibiting SOAG after SO removal. However, most patients may require antiglaucoma medication during the follow-up, particularly within the first 2 postoperative years.
Comparing an All-RN Unit to a Mixed-Skill Unit at a Hospital
Authors: Dzikowicz Dillon J. , Schmitt Linda A. , Gastle Karen , Skermont Amanda , Carey Mary G. 
Published: November 2020

OBJECTIVE
The aim of this study was to assess the differences in patient complications as well as patient and staff satisfaction between a mixed-skill unit and an all–registered nurse (RN) unit.

BACKGROUND
It is recognized that nursing care delivered by RNs results in better outcomes; however, more evidence is needed to support a change to an all-RN unit.

METHODS
A mixed unit with RNs and unlicensed assistive personnel was compared with an all-RN unit. Each unit had similar resources. Patient complications and patient and staff satisfaction were measured. Patient complications were reported in terms of 1,000 patient days over the study period to minimize noise fluctuations; t test and χ
2 compared means and frequencies, respectively.

RESULTS
The all-RN unit had a lower prevalence of patient complications. Patients reported better pain management, and nurse explanation, and reported higher satisfaction on the all-RN unit.

CONCLUSIONS
An all-RN unit provided superior outcomes compared with a mixed-skill unit without additional costs.
Application of Transcranial Color-coded Duplex Sonography in the Diagnosis and Management of Straight Sinus Thrombosis With Dural Arteriovenous Fistulae
Authors: Zhu Xueli , Gong Xiping , Zhang Bin , Zhou Shengjun , Wang Fumin , He Wen 
Published: November 2020

Introduction:
Transcranial color-coded duplex sonography (TCCS) with and without ultrasound contrast agent has been used to diagnose cerebral venous thrombosis, however, no experience in the diagnosis of patients with cerebral venous thrombosis and with dural arteriovenous fistula (dAVF) by contrast-enhanced TCCS has been reported yet.

Case Report:
The authors reported a 49-year-old male patient with straight sinus (StS) thrombosis and dAVF. Plain TCCS and contrast-enhanced TCCS demonstrated the direct presentation of the selected feeder and drainage veins of the dAVFs, arterialized venous flow waveform, and an enlarged optic nerve sheath diameter, indicating an increased intracranial pressure, and a filling defect in the StS even after administration of an ultrasound contrast agent. After intravascular thrombolysis and blockage of 2 feeders of the dAVF, TCCS still showed retrograde flow direction in the left basal vein and significantly elevated flow velocity in the StS, reflecting a high venous pressure caused by a high volume of arteriovenous shunt and severe stenosis in the StS. The patient’s clinical manifestation did not substantially improve until 3 stents were implanted in the StS, and TCCS unveiled that the stents were well filled with flow signal, and the flow velocity in the StS dramatically decreased.

Conclusions:
TCCS could provide reliable data about the feeder and drainage veins of dAVF in our case. The extent of an increase in venous flow velocity may be closely associated with clinical manifestations, which may influence therapy. Moreover, TCCS possesses a unique advantage in terms of evaluating the patency of the stents compared with other neuroimaging techniques.
Hirayama Disease Presenting as 4-Limb Paresthesia
Authors: Fereidan-Esfahani Mahboobeh , Tobin William Oliver 
Published: November 2020

Introduction:
Hirayama disease is a rare clinical entity that presents typically as a unilateral, slowly progressive arms weakness, mostly occurring in young men.

Case Report:
We report a case of Hirayama disease in a 20-year-old man presenting with a 4-year history of progressive paresthesia starting in his left arm, progressing to the right arm 1 year later. Four months before the presentation, he experienced bilateral foot paresthesias. Examination revealed weakness of the abductor digiti minimi, hallux extension weakness, and postural tremor bilaterally. He had hypersensitivity to pinprick in both hands with ulnar and median distribution. Sensory examination in the legs was normal. He had a postural tremor in both hands, which worsened on neck flexion. Spinal fluid analysis, including oligoclonal band testing, was normal. Electromyography demonstrated bilateral chronic C7 and C8 radiculopathies. Laboratory tests were normal. Flexion-extension magnetic resonance imaging demonstrated laxity of the dura and ligamentum flavum, with compression of cervical cord, maximal at C5-C6 in neck flexion.

Conclusions:
Laxity of the posterior dura during neck flexion has been postulated to lead to asymmetric lower cervical cord atrophy. Involvement of all 4 limbs is rare, and the condition can be mistaken for progressive multiple sclerosis.
Predicting the Need For Vasopressors in the Intensive Care Unit Using an Attention Based Deep Learning Model
Authors: Kwak Gloria Hyunjung , Ling Lowell , Hui Pan 
Published: November 2020

ABSTRACT

Background:
Previous models on prediction of shock mostly focused on septic shock and often required laboratory results in their models. The purpose of this study was to use deep learning approaches to predict vasopressor requirement for critically ill patients within 24 h of intensive care unit (ICU) admission using only vital signs.

Methods:
We used data from the Medical Information Mart for Intensive Care III database and the eICU Collaborative Research Database to develop a vasopressor prediction model. We performed systematic data preprocessing using matching of cohorts, oversampling, and imputation to control for bias, class imbalance, and missing data. Bidirectional long short-term memory (Bi-LSTM), a multivariate time series model, was used to predict the need for vasopressor therapy using serial physiological data collected 21 h prior to prediction time.

Results:
Using data from 10,941 critically ill patients from 209 ICUs, our model achieved an initial area under the curve of 0.96 (95% CI 0.96–0.96) to predict the need for vasopressor therapy in 2 h within the first day of ICU admission. After matching to control class imbalance, the Bi-LSTM model had area under the curve of 0.83 (95% CI 0.82–0.83). Heart rate, respiratory rate, and mean arterial pressure contributed most to the model.

Conclusions:
We used Bi-LSTM to develop a model to predict the need for vasopressor for critically ill patients for the first 24 h of ICU admission. With attention mechanism, respiratory rate, mean arterial pressure, and heart rate were identified as key sequential determinants of vasopressor requirements.
ProteoMill: Efficient network-based functional analysis portal for proteomics data
Authors: Rydén M , Englund M , Ali N 
Published: November 2020

AbstractFunctional analysis has become a common approach to incorporate biological knowledge into the analysis of omics data, and to explore molecular events that govern a disease state. It is though only one step in a wider analytical pipeline that typically requires use of multiple individual analysis software. There is currently a need for a well-integrated omics analysis tool that performs all the steps. The ProteoMill portal is developed as an R Shiny application and integrates all necessary steps from data-upload, converting identifiers, to quality control, differential expression and network-based functional analysis into a single fast, interactive easy to use workflow. Further, it maintains annotation data sources up to date, overcoming a common problem with use of outdated information, and seamlessly integrates multiple R-packages for an improved user-experience. The functionality provided in this software can benefit researchers by facilitating the exploratory analysis of proteomics data.ProteoMill is available for free athttps://proteomill.com.
SlSWEET15 exports sucrose from phloem and seed coat in tomato to supply carbon for fruit and seed development
Authors: Ko Han-Yu , Ho Li-Hsuan , Neuhaus H. Ekkehard , Guo Woei-Jiun 
Published: November 2020

ABSTRACTTomato, an important fruit crop worldwide, requires efficient sugar allocation for fruit development. However, molecular mechanisms for sugar import to fruits remain poorly understood. Expression of SWEET (Sugars Will Eventually be Exported Transporters) proteins is closely linked with hexose ratio in tomato fruits and may be involved in sugar allocation. Here, using quantitative PCR, we discovered thatSlSWEET15was highly expressed in developing fruits compared to vegetative organs. Based onin situhybridization and GUS fusion analyses,SlSWEET15 proteins accumulated in vascular tissues and seed coats, major sites of sucrose unloading in fruits. LocalizingSlSWEET15-GFP to the plasma membrane supported its putative role in apoplasmic sucrose unloading. The sucrose transport activity ofSlSWEET15 was confirmed by complementary growth assays in a yeast mutant. Elimination of theSlSWEET15 function by CRISPR/cas9 gene editing significantly decreased average sizes and weights of fruits, with severe defects in seed filling and embryo development. Together, we confirmed the role ofSlSWEET15 in mediating sucrose efflux from the releasing phloem to the fruit apoplasm and subsequent import into parenchyma cells during fruit development. Furthermore,SlSWEET15-mediated sucrose efflux was also required for sucrose unloading from the seed coat to the developing embryo.One-sentence SummarySlSWEET15, a specific sucrose uniporter in tomato, mediates apoplasmic sucrose unloading from releasing phloem cells and seed coat for carbon supply during fruit expansion and seed filling.
Pushing Raman spectroscopy over the edge: purported signatures of organic molecules in fossils are instrumental artefacts
Authors: Alleon Julien , Montagnac Gilles , Reynard Bruno , Brulé Thibault , Thoury Mathieu , Gueriau Pierre 
Published: November 2020

AbstractClaims for the widespread preservation of fossilized biomolecules in many fossil animals have recently been reported in six studies, based on Raman microspectroscopy. Here, we show that the putative Raman signatures of organic compounds in these fossils are actually instrumental artefacts resulting from intense background luminescence. Raman spectroscopy relies upon the detection of photons scattered inelastically by matter as a result of its interaction with a laser beam. For many natural materials, this interaction also generates a luminescence signal that is often orders of magnitude more intense than the light produced by Raman scattering. Such luminescence, coupled with the transmission properties of the spectrometer, induced quasi-periodic ripples in the measured spectra that have been incorrectly interpreted as Raman signatures of organic molecules. Although several analytical strategies have been developed to overcome this common issue, Raman microspectroscopy as used in the studies questioned here cannot be used to identify fossil biomolecules.
Evaluating and Improving SSU rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys
Authors: McNichol Jesse , Berube Paul M. , Biller Steven J. , Fuhrman Jed A. 
Published: November 2020

AbstractSmall subunit ribosomal RNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly-used primers with > 300 million rRNA gene sequences retrieved from globally-distributed marine metagenomes. The best-performing primers when comparing to 16S rRNA of Bacteria and Archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering Cyanobacteria and Chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA-specific; 82%) – demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R2=0.98, n=272), indicating amplicons can produce equally accurate community composition data versus shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly-completely universal primer set that could accurately quantify biogeochemically-important taxa in ecosystems ranging from the deep-sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data.Significance StatementPCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time, but will only work optimally if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally-distributed short-read oceanic metagenomes. Our results demonstrate primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides and present a software pipeline that can guide rational design of primers for any environment with available meta’omic data.
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
Authors: Sheng Xin , Ma Ziyuan , Wu Junnan , Liu Hongbo , Qiu Chengxiang , Miao Zhen , Seasock Matthew J. , Palmer Matthew , Shin Myung K. , Duffin Kevin L. , Pullen Steven S. , Edwards Todd L. , Hellwege Jacklyn N. , Hung Adriana M. , Li Mingyao , Voight Benjamin , Coffman Thomas , Brown Christopher D. , Susztak Katalin 
Published: November 2020

AbstractThe functional interpretation of GWAS remains challenging due to cell-type dependent influences of genetic variants.Here, we generated comprehensive maps of expression quantitative trait loci (eQTL) for 659 microdissected human kidney samples and identified cell-type eQTLs by mapping interactions between cell type abundance and genotype. Separately, we generated single cell open chromatin maps (by snATAC-seq) for human kidney samples. We highlight critical enrichment of proximal tubules in kidney function and endothelial cells and distal tubule segments in blood pressure by partitioning heritability using stratified LD-score regression to integrate GWAS with scRNA-seq and snATAC-seq data. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of the most commonly used antihypertensive and renal protective drugs and identifies drug repurposing opportunities for kidney disease.One Sentence SummaryWe define causal cell types, genes and mechanism for kidney dysfunction.
DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
Authors: Yin Qijin , Cao Xusheng , Fan Rui , Liu Qiao , Jiang Rui , Zeng Wanwen 
Published: November 2020

AbstractComputational approaches for accurate prediction of drug interactions, such as drug-drug interactions (DDIs) and drug-target interactions (DTIs), are highly demanded for biochemical researchers due to the efficiency and cost-effectiveness. Despite the fact that many methods have been proposed and developed to predict DDIs and DTIs respectively, their success is still limited due to a lack of systematic evaluation of the intrinsic properties embedded in the corresponding chemical structure. In this paper, we develop a deep learning framework, named DeepDrug, to overcome the above limitation by using residual graph convolutional networks (RGCNs) and convolutional networks (CNNs) to learn the comprehensive structural and sequential representations of drugs and proteins in order to boost the DDIs and DTIs prediction accuracy. We benchmark our methods in a series of systematic experiments, including binary-class DDIs, multi-class/multi-label DDIs, binary-class DTIs classification and DTIs regression tasks using several datasets. We then demonstrate that DeepDrug outperforms state-of-the-art methods in terms of both accuracy and robustness in predicting DDIs and DTIs with multiple experimental settings. Furthermore, we visualize the structural features learned by DeepDrug RGCN module, which displays compatible and accordant patterns in chemical properties and drug categories, providing additional evidence to support the strong predictive power of DeepDrug. Ultimately, we apply DeepDrug to perform drug repositioning on the whole DrugBank database to discover the potential drug candidates against SARS-CoV-2, where 3 out of 5 top-ranked drugs are reported to be repurposed to potentially treat COVID-19. To sum up, we believe that DeepDrug is an efficient tool in accurate prediction of DDIs and DTIs and provides a promising insight in understanding the underlying mechanism of these biochemical relations. The source code of the DeepDrug can be freely downloaded fromhttps://github.com/wanwenzeng/deepdrug.
The H3.3K27M oncohistone antagonizes reprogramming in Drosophila
Authors: Ahmad Kami , Henikoff Steven 
Published: November 2020

AbstractDevelopment proceeds by the activation of genes by transcription factors and the inactivation of others by chromatin-mediated gene silencing. In some cases development can be reversed or redirected by mis-expression of master regulator transcription factors. This must involve the activation of previously silenced genes, and such developmental aberrations are thought to underlie a variety of cancers. Here, we express the wing-specific Vestigial master regulator to reprogram the developing eye, and test the role of silencing in reprogramming using an H3.3K27M oncohistone mutation that dominantly inhibits histone H3K27 trimethylation. We find that expression of the oncohistone blocks eye-to-wing reprogramming. CUT&Tag chromatin profiling of mutant tissues shows that H3K27me3 domains are globally reduced with oncohistone expression, suggesting that previous developmental programs must be silenced for effective transformation. Strikingly, mis-expressed Vg and H3.3K27M synergize to stimulate overgrowth of eye tissue, a phenotype that resembles that of mutations in Polycomb Repressive Complex 1 components. Our results imply that growth dysregulation can result from the simple combination of crippled silencing and transcription factor mis-expression, an effect that may explain the origins of oncohistone-bearing cancers.
A new microfluidic concept for successfulin vitroculture of mouse embryos
Authors: Mancini V. , McKeegan P.J , Rutledge A.C. , Codreanu S.G. , Sherrod S.D. , McLean J.A. , Picton H.M , Pensabene V. 
Published: November 2020

ABSTRACTInnovative techniques for gene editing have enabled accurate animal models of human diseases to be established. In order for these methods to be successfully adopted in the scientific community, the optimization of procedures used for breeding genetically altered mice is required. Among these, thein vitrofertilization (IVF) procedure is still suboptimal and the culture methods do not guarantee the development of competent embryos. Critical aspects in traditionalin vitroembryo culture protocols include the use of mineral oil and the stress induced by repetitive handling of the embryos.A new microfluidic system was designed to allow for efficientin vitroculture of mouse embryos. Harmful fluidic stress and plastic toxicity were excluded by completing the industry gold standard Mouse Embryo Assay. The potential competence of the embryos developed in the device was quantified in terms of blastocyst rate, outgrowth assay, energy substrate metabolism and expression of genes related to implantation potential.Mass spectrometry analyses identified plastic-related compounds released in medium, and confirmed leaching of low molecular weight species into the culture medium that might be associated to un-crosslinked PDMS.Finally, these data show the potential for the system to study preimplantation embryo development and to improve human IVF techniques.