bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comparative Study of Finger Pulp Reconstruction Using Free Distal Ulnar Artery Perforator Flaps and Reverse Dorsal Homodigital Island Flaps
Authors: Tu Qiming , Liu Shaodong , Chen Tingxiang , Li Shi , Yan Hede , Li Zhijie 
Published: November 2019

Purpose
This study aimed to compare and analyze the outcomes of finger reconstruction using free distal ulnar artery perforator (FDUAP) and reverse dorsal homodigital island (RDHI) flaps.

Methods
The study included 27 patients with finger pulp defects that were reconstructed using FDUAP or RDHI flaps. Standardized assessment of outcomes included objective sensory recovery, duration of operation, range of motion in the repaired fingers, pain at the reconstructed finger pulps and donor sites, and recovery time before returning to work. Subjective assessment of outcomes included the cold intolerance, aesthetic appearance, and functional recovery.

Results
All flaps in the series showed complete survival. The average surgical time for the RDHI flaps was significantly smaller than that for the FDUAP flaps. Sensory recovery was significantly better with FDUAP flaps than with RAHI flaps. No significant differences were detected between the 2 procedures regarding range of motion, cold intolerance, or pain of the injured finger pulps and donor sites. The outcomes of aesthetic result and functional recovery satisfied all patients. Optimal cosmetic satisfaction was obtained in the FDUAP flap group.

Conclusions
Although both types of flaps offer a satisfactory approach for finger reconstruction with small-to-medium defects, FDUAP flaps are more suitable for such operations because of the better sensory reconstruction and aesthetic results.
Computer-Aided-Design/Computer-Aided-Manufacturing Titanium Cranioplasty in a Child: Critical Appraisal
Authors: Zegers Thomas , Koper David , Lethaus Bernd , Kessler Peter , ter Laak-Poort Mariel 
Published: November 2019

Abstract
Large skull bone defects of the cranial vault can result from various reasons. Reconstruction of these defects is performed for protective and aesthetic reasons but is also required for adequate intracranial homeostasis. Computer-aided-design/computer-aided-manufacturing (CAD/CAM) patient-specific skull implants have become the most valuable alternative to the traditional methods of reconstruction and a growing number of publications is dealing with this topic in adults. Literature related to the application of these implants in pediatric cranioplasty is, however, still scarce.
The authors present a case of a 9-year-old boy, where cranioplasty using a CAD/CAM additive manufactured titanium implant led to improvement of symptoms attributed to cerebrospinal fluid circulation problems and intracranial homeostasis disbalance. The authors further reflect on what the role of cranioplasty should be in the therapeutic treatment plan.
Persistent Opioid Use After Combat Injury and Subsequent Long-term Risk of Abuse
Authors: Beyer Carl A. , Poltavskiy Eduard , Walker Lauren E. , Pettey Warren , Suo Ying , Redd Andrew , Rittel Alex G. , Kazanis William H. , Dunham Jacob R. , Zarzabal Lee A. , Rutter W. Cliff , Sim Alan , Watrous Jessica R. , Howard Jeffrey T. , Janak Jud C. , Stewart Ian J. , Gundlapalli Adi 
Published: November 2019

Objective:
To determine whether persistent opioid use after injury is associated with subsequent long-term development of clinically recognized opioid abuse.

Summary Background Data:
Opioid abuse is an epidemic in the United States and trauma can initiate persistent use; however, it remains unclear whether persistent opioid use contributes to the subsequent development of opioid abuse. The care of combat casualties by the Departments of Defense and Veterans Affairs uniquely allows investigation of this long-term outcome.

Methods:
This retrospective cohort study randomly selected 10,000 battle-injured United States military personnel. We excluded patients who died during initial hospitalization or within 180 days of discharge, had a preinjury opioid abuse diagnosis, or had missing data in a preselected variable. We defined persistent opioid use as filling an opioid prescription 3 to 6 months after discharge and recorded clinically recognized opioid abuse using relevant diagnosis codes.

Results:
After exclusion, 9284 subjects were analyzed, 2167 (23.3%) of whom developed persistent opioid use. During a median follow-up time of 8 years, 631 (6.8%) patients developed clinically recognized opioid abuse with a median time to diagnosis of 3 years. Injury severity and discharge opioid prescription amount were associated with persistent opioid use after trauma. After adjusting for patient and injury-specific factors, persistent opioid use was associated with the long-term development of clinically recognized opioid abuse (adjusted hazard ratio, 2.39; 95% confidence interval, 1.99–2.86).

Conclusions:
Nearly a quarter of patients filled an opioid prescription 3 to 6 months after discharge, and this persistent use was associated with long-term development of opioid abuse.
Prophylaxis of Wound Infections-antibiotics in Renal Donation (POWAR)
Authors: Ahmed Zubir , Uwechue Raphael , Chandak Pankaj , van Dellen David , Barwell Jamie , Heap Sarah , Szabo Laszlo , Hemsley Carolyn , Olsburgh Jonathon , Kessaris Nicos , Mamode Nizam 
Published: November 2019

Background:
Postoperative infection after hand-assisted laparoscopic donor nephrectomy (HALDN) confers significant morbidity to a healthy patient group. Current UK guidelines cite a lack of evidence for routine antibiotic prophylaxis. This trial assessed if a single preoperative antibiotic dose could reduce post HALDN infections.

Methods:
Eligible donors were randomly and blindly allocated to preoperative single-dose intravenous co-amoxiclav or saline. The primary composite endpoint was clinical evidence of any postoperative infection at 30 days, including surgical site infection (SSI), urinary tract infection (UTI), and lower respiratory tract infection (LRTI).

Findings:
In all, 293 participants underwent HALDN (148 antibiotic arm and 145 placebo arm). Among them, 99% (291/293) completed follow-up. The total infection rate was 40.7% (59/145) in the placebo group and 23% (34 of 148) in the antibiotic group (P = 0.001). Superficial SSIs were 20.7% (30/145 patients) in the placebo group versus 10.1% (15/148 patients) in the antibiotic group (P = 0.012). LRTIs were 9% (13/145) in the placebo group and 3.4% (5/148) in the antibiotic group (P = 0.046). UTIs were 4.1% (6/145) in the placebo group and 3.4% (5/148) in the antibiotic group (P = 0.72).
Antibiotic prophylaxis conferred a 17.7% (95% confidence interval 7.2%–28.1%), absolute risk reduction in developing postoperative infection, with 6 donors requiring treatment to prevent 1 infection.

Interpretation:
Single-dose preoperative antibiotic prophylaxis dramatically reduces post-HALDN infection rates, mainly impacting SSIs and LRTIs.
Incidence and Risk Factors of Postoperative Mortality and Morbidity After Elective Versus Emergent Abdominal Surgery in a National Sample of 8193 Patients With Cirrhosis
Authors: Johnson Kay M. , Newman Kira L. , Green Pamela K. , Berry Kristin , Cornia Paul B. , Wu Peter , Beste Lauren A. , Itani Kamal , Harris Alex H. S. , Kamath Patrick S. , Ioannou George N. 
Published: November 2019

Objective:
To describe the incidence and risk factors for mortality and morbidity in patients with cirrhosis undergoing elective or emergent abdominal surgeries.

Background:
Postoperative morbidity and mortality are higher in patients with cirrhosis; variation by surgical procedure type and cirrhosis severity remain unclear.

Methods:
We analyzed prospectively-collected data from the Veterans Affairs (VA) Surgical Quality Improvement Program for 8193 patients with cirrhosis, 864 noncirrhotic controls with chronic hepatitis B infection, and 5468 noncirrhotic controls without chronic liver disease, who underwent abdominal surgery from 2001 to 2017. Data were analyzed using random-effects models controlling for potential confounders.

Results:
Patients with cirrhosis had significantly higher 30-day mortality than noncirrhotic patients with chronic hepatitis B [4.4% vs 1.3%, adjusted odds ratio (aOR) 2.80, 95% confidence interval (CI) 1.57–4.98] or with no chronic liver disease (0.8%, aOR 4.68, 95% CI 3.27–6.69); mortality difference was highest in patients with Model for End-stage Liver Disease (MELD) score ≥10. Among patients with cirrhosis, postoperative mortality was almost 6 times higher after emergent rather than elective surgery (17.2% vs. 2.1%, aOR 5.82, 95% CI 4.66–7.27). For elective surgeries, 30-day mortality was highest after colorectal resection (7.0%) and lowest after inguinal hernia repair (0.6%). Predictors of postoperative mortality included cirrhosis-related characteristics (high MELD score, low serum albumin, ascites, encephalopathy), surgery-related characteristics (emergent vs elective, type of surgery, intraoperative blood transfusion), comorbidities (chronic obstructive pulmonary disease, cancer, sepsis, ventilator dependence, functional status), and age.

Conclusions:
Accurate preoperative risk assessments in patients with cirrhosis should account for cirrhosis severity, comorbidities, type of procedure, and whether the procedure is emergent versus elective.
Neuroprogesterone signals through Src kinase within RP3V neurons to induce the luteinizing hormone surge in female rats
Authors: Chuon Timbora , Feri Micah , Carlson Claire , Ondrejik Sharity , Micevych Paul , Sinchak Kevin 
Published: November 2019

ABSTRACTNeural circuits in female rats are exposed to estradiol and sequential progesterone to regulate the luteinizing hormone (LH) surge and thus ovulation. Estradiol induces progesterone receptors (PGRs) in rostral periventricular region of the third ventricle (RP3V) kisspeptin neurons, and positive feedback estradiol concentrations induce neuroprogesterone (neuroP) synthesis in hypothalamic astrocytes that signal to PGRs expressed in kisspeptin neurons to trigger the LH surge. We tested the hypothesis that neuroP-PGR signals through Src family kinase (Src) to trigger the LH surge. As in vitro, PGR and Src are co-expressed in RP3V neurons. Estradiol treatment increased the number of PGR immunopositive cells and PGR and Src colocalization. Infusion of the Src inhibitor (PP2) into the RP3V, attenuated the LH surge measured by ELISA in trunk blood collected 53 hours post-EB injection. While PP2 reduced the LH surge in 50 μg EB treated ovariectomized/adrenalectomized (ovx/adx) rats, activation of either PGR or Src in 2μg EB primed animals significantly elevated LH concentrations compared with DMSO treated ovx/adx rats. These results support the importance of Src in the estradiol and neuroP triggering of the LH surge.
Fat food exacerbates post-prandial hypothalamic inflammation involving GFAP+ cells and microglia
Authors: Cansell C. , Stobbe K. , Le Thuc O. , Mosser CA. , Ben-Fradj S. , Leredde J. , Lebeaupin C. , Debayle D. , Fleuriot L. , Brau F. , Devaux N. , Benani A. , Audinat E. , Blondeau N. , Nahon JL. , Rovère C. 
Published: November 2019

AbstractIn humans, obesity was associated with brain inflammation and glial cell proliferation. Studies in rodents showed that glial cell proliferation occurs within 24 hours of high-fat diet (HFD) consumption, before obesity development. This proliferation was mainly observed in the hypothalamus (HT), a crucial brain structure for controlling body weight. Therefore, we sought to characterize the post-prandial HT inflammatory response to 1-3-6 hours exposure to a standard diet and HFD. HFD exposure increased gene expression of astrocyte and microglial marker (GFAP and Iba1) compare to standard treated mice and induced morphological modifications of microglial cells in HT. This remodeling was associated with higher expression of inflammatory genes and differential activation of hypothalamic neuropeptides involved in energy balance regulation. DREADD and PLX5622 technologies, used to modulate GFAP-positive or microglial cells activity respectively, showed that both glial cell types are involved in hypothalamic post-prandial inflammation, but in a different time frame and with a diet specificity Thus, an exacerbated post-prandial inflammation in brain might predispose individuals to obesity and needs to be characterized to address this worldwide crisis.
Transcranial Near-Infrared Light: Dose-Dependent Effects on EEG Oscillations but not Cerebral Blood Flow
Authors: Spera Vincenza , Sitnikova Tatiana , Ward Meredith J. , Farzam Parya , Hughes Jeremy , Bui Eric , Maiello Marco , De Taboada Luis , Hamblin Michael R. , Franceschini Maria Angela , Cassano Paolo 
Published: November 2019

ABSTRACTObjectiveOur objective was to assess whether transcranial photobiomodulation (tPBM) with near-infrared light (NIR) shows modulatory effects on cerebral electrical activity through electroencephalogram (EEG) and cerebral blood flow (CBF).BackgroundtPBM has emerged as a novel intervention for several neuropsychiatric conditions due to its neuroprotective and neuroenhancement effects.MethodsWe conducted a single-blind, sham-controlled pilot study to test the effect of continuous (c-tPBM), pulse (p-tPBM) and sham (s-tPBM) transcranial photobiomodulation on EEG oscillations and CBT using diffuse correlation spectroscopy (DCS) in a sample of ten healthy subjects [6 F/ 4 M; mean age 28.6 ± 12.9 (SD) years]. c-tPBM NIR (830 nm; 54.8 mW/cm²; 65.8 J/cm²; 2.3 kJ) and p-tPBM (830 nm; 10Hz; 54.8 mW/cm²; 33%; 21.7 J/cm²; 0.8 kJ) were delivered concurrently to the frontal areas (F4, Fp2, Fp1, F3 - total surface 35.8 cm²) by four LED clusters (TPBM-1000 Litecure). EEG and DCS recordings were performed weekly before, during, and after each tPBM session (in sequence: c-tPBM, s-tPBM and p-tPBM).ResultsOnly c-tPBM significantly boosted gamma (t = 3.02, df = 7, p < .02) and beta (t = 2.91, df = 7, p < .03) EEG spectral powers in eyes-open recordings and gamma power (t = 3.61, df = 6, p < .015) in eyes-closed recordings, with the largest effects in the posterior regions. There was no significant effect of NIR-tPBM on CBF compared to sham.ConclusionsOur data suggest a dose-dependent effect of tPBM with NIR (c-tPBM) on cerebral gamma and beta neuronal activity. Altogether, our findings support the neuromodulatory effect of transcranial NIR.
Experimental and simulated CO2 responses of photosynthesis in leaves of Hippophae rhamnoides L. under different soil water conditions
Authors: Wu Qin , Li Cheng , Chen Qiang 
Published: November 2019

AbstractCO2 concentrations and soil moisture conditions seriously affect tree growth and physiological mechanisms. CO2 responses of photosynthesis are an important part of plant physiology and ecology research. This study investigated the photosynthetic CO2 responses in the leaves of two-year-old Hippophae rhamnoides L. under eight soil water conditions in a semi-arid loess hilly region, and discussed the quantitative relationship between CO2 responses and soil moisture. CO2 response curves and parameters were fitted using a rectangular hyperbola model, non-rectangular hyperbola model, exponential equation, and modified rectangular hyperbola model. Results revealed that the relative soil water content (RWC) required to maintain a high photosynthetic rate (Pn) and carboxylation efficiency (CE) ranged from 42.8% to 83.2%. When RWC fell outside these ranges, the photosynthetic capacity (Pnmax), CE, and CO2 saturation point (CSP) decreased. CO2 response curves and three parameters, CE, CO2 compensation point (Γ), and photorespiration rate (Rp), were well fitted by the four models when RWC was appropriate. When RWC exceeded the optimal range, only the modified rectangular hyperbola model fitted the CO2 response curves and photosynthetic parameters better.
Training deep neural density estimators to identify mechanistic models of neural dynamics
Authors: Gonçalves Pedro J. , Lueckmann Jan-Matthis , Deistler Michael , Nonnenmacher Marcel , Öcal Kaan , Bassetto Giacomo , Chintaluri Chaitanya , Podlaski William F. , Haddad Sara A. , Vogels Tim P. , Greenberg David S. , Macke Jakob H. 
Published: November 2019

AbstractMechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators— trained using model simulations— to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features, and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.
Topaz-Denoise: general deep denoising models for cryoEM and cryoET
Authors: Bepler Tristan , Kelley Kotaro , Noble Alex J. , Berger Bonnie 
Published: November 2019

AbstractCryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. Denoising cryoEM images can not only improve downstream analysis but also accelerate the time-consuming data collection process by allowing lower electron dose micrographs to be used for analysis. Here, we present Topaz-Denoise, a deep learning method for reliably and rapidly increasing the SNR of cryoEM images and cryoET tomograms. By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process. The general model we present is able to denoise new datasets without additional training. Denoising with this model improves micrograph interpretability, enabling us to solve the first 3D single particle closed and partially open structures of clustered protocadherin, an elongated particle with previously-elusive views. We then show for the first time that low dose collection, enabled by Topaz-Denoise, improves downstream analysis in addition to reducing data collection time. We also present the first general 3D denoising model for cryoET. Topaz-Denoise and pre-trained general models are now included in Topaz. We expect that Topaz-Denoise will be of broad utility to the cryoEM community for improving micrograph and tomogram interpretability and accelerating analysis.
HIP IMO Report: Analyzing Phenotypic Properties of Bladder Cancer Using Ordinary Differential Equation (ODE) Models
Authors: Sherwin Benjamin 
Published: November 2019

AbstractBladder cancer is composed of proliferative and immunogenic phenotypes, which ultimately play a significant role in the growth of the tumor. By using ordinary differential equation models, this paper models the impact of high and low immunogenic cell populations on non-muscle invasive bladder cancer when treated with and without the Bacillus Calmette-Guerin vaccine. Furthermore, this paper models the impact that the Bacillus Calmette-Guerin vaccine has on inflammatory cytokines, which inhibit the growth of tumors by stimulating an immune response. We focus primarily on how the immunogenicity phenotype impacts population dynamics in non-muscle invasive bladder cancer.
Visualization of the HIV-1 Env Glycan Shield Across Scales
Authors: Berndsen Zachary T. , Chakraborty Srirupa , Wang Xiaoning , Cottrell Christopher A. , Torres Jonathan L. , Diedrich Jolene K. , López Cesar A. , Yates John R. , van Gils Marit J. , Paulson James C. , Gnanakaran S , Ward Andrew B. 
Published: November 2019

AbstractThe dense array of N-linked glycans on the HIV-1 Envelope Glycoprotein (Env), known as the “glycan shield”, is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure-function analysis. Here we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass-spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of inter-glycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same CHO cell line used for GMP production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner we found that highly connected glycan clusters are resistant to digestion and help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion.Significance StatementThe HIV-1 Env “glycan shield” masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure-function description. Using a complementary approach of cryo-EM, computational modeling, and mass-spectrometry we show how heterogeneity and dynamics affect glycan shield structure across scales. Our combined approach facilitated the development of new cryo-EM data analysis methods and allowed for validation of models against experiment. Comparison of Env across a range of glycosylation states revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion.
RNA G-quadruplex structures exist and function in vivo
Authors: Yang Xiaofei , Cheema Jitender , Zhang Yueying , Deng Hongjing , Duncan Susan , Umar Mubarak Ishaq , Zhao Jieyu , Liu Qi , Cao Xiaofeng , Kwok Chun Kit , Ding Yiliang 
Published: November 2019

AbstractGuanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA G-quadruplexes are proposed to exist in vivo and are suggested to be associated with important biological relevance. However, there is a lack of direct evidence for RNA G-quadruplex formation in living cells. Therefore, it is unclear whether any purported functions are associated with the specific sequence content or the formation of an RNA G-quadruplex structure. Here, we profiled the landscape of those guanine-rich regions with the in vitro folding potential in the Arabidopsis transcriptome. We found a global enrichment of RNA G-quadruplexes with two G-quartets whereby the folding potential is strongly influenced by RNA secondary structures. Using in vitro and in vivo RNA chemical structure profiling, we determined that hundreds of RNA G-quadruplex structures are strongly folded in both Arabidopsis and rice, providing direct evidence of RNA G-quadruplex formation in living eukaryotic cells. Subsequent genetic and biochemical analysis showed that RNA G-quadruplex folding was sufficient to regulate translation and modulate plant growth. Our study reveals the existence of RNA G-quadruplex in vivo, and indicates that RNA G-quadruplex structures act as important regulators of plant development and growth.