bluuebunny/crossref_metadata_2025_split huggingface dataset:
A model to illustrate the potential pairing of animal biotelemetry with individual-based modeling
Authors: Brosnan Ian G. , Welch David W. 
Published: December 2020

Abstract
Background
Animal biotelemetry and individual-based modeling (IBM) are natural complements, but there are few published examples where they are applied together to address fundamental or applied ecological questions. Existing studies are often found in the modeling literature and frequently re-use small datasets collected for purposes other than the model application. Animal biotelemetry can provide the robust measurements that capture relevant ecological patterns needed to parameterize, calibrate, and assess hypotheses in IBMs; together they could help meet demand for predictive modeling and decision-support in the face of environmental change.

Results
We used an simple exemplar IBM that uses spatio-temporal movement patterns of 103 acoustic-tagged juvenile yearling Chinook salmon (Oncorhynchus tshawytscha), termed ‘smolts’, to quantitatively assess plausibility of two migratory strategies that smolts are hypothesized to use while migrating north through the plume of the Columbia River (United States of America). We find that model smolts that seek to maximize growth demonstrate movement patterns consistent with those of tagged smolts. Model smolts that seek to move quickly out of the plume region by seeking favorable currents do not reproduce the same patterns.

Conclusions
Animal biotelemetry and individual-based modeling are maturing fields of inquiry. Our hope is that this model description and the basic analytical techniques will effectively illustrate individual-based models for the biotelemetry community, and perhaps inspire new collaborations between biotelemetry researchers and individual-based modelers.
Isotope-reinforced polyunsaturated fatty acids improve Parkinson’s disease-like phenotype in rats overexpressing α-synuclein
Authors: Beal M. Flint , Chiluwal Jayandra , Calingasan Noel Y. , Milne Ginger L. , Shchepinov Mikhail S. , Tapias Victor 
Published: December 2020

AbstractLipid peroxidation is a key to a portfolio of neurodegenerative diseases and plays a central role in α-synuclein (α-syn) toxicity, mitochondrial dysfunction and neuronal death, all key processes in the pathogenesis of Parkinson’s disease (PD). Polyunsaturated fatty acids (PUFAs) are important constituents of the synaptic and mitochondrial membranes and are often the first molecular targets attacked by reactive oxygen species (ROS). The rate-limiting step of the chain reaction of ROS-initiated PUFAs autoxidation involves hydrogen abstraction at bis-allylic sites, which can be slowed down if hydrogens are replaced with deuteriums. In this study, we show that targeted overexpression of human A53T α-syn using an AAV vector unilaterally in the rat substantia nigra reproduces some of pathological features seen in PD patients. Chronic dietary supplementation with deuterated PUFAs (D-PUFAs), specifically 0.8% D-linoleic and 0.3% H-linolenic, produced significant disease-modifying beneficial effects against α-syn-induced motor deficits, synaptic pathology, oxidative damage, mitochondrial dysfunction, disrupted trafficking along axons, inflammation and DA neuronal loss. These findings support the clinical evaluation of D-PUFAs as a neuroprotective therapy for PD.
A solitary hypothalamic metastasis from prostatic cancer mimicking a giant thrombotic aneurysm and presenting with intraventricular hemorrhage and acute hydrocephalus: a case report
Authors: Saadatpour Zarhra , Rezaei Ali , Singhal Aparna , Sotoudeh Houman , Tavakol Kamran 
Published: December 2020

Abstract
Background
Despite the high prevalence of prostate cancer, its brain parenchymal metastasis is not common and intracranial hemorrhage due to such a metastasis is even less common. This report presents a challenging case of solitary brain metastasis secondary to prostate cancer that gave rise to intraventricular hemorrhage and acute hydrocephalus mimicking a giant aneurysm.

Case presentation
A 77-year-old man with a history of prostate cancer, hypertension, and morbid obesity presented to the emergency room with a severe headache. He was afebrile with a blood pressure of 144/79 mmHg, alert, without any sign of sensory or motor deficit. Shortly after admission, he became unresponsive and was immediately intubated. His blood tests revealed hypernatremia at 154 mmol/L; otherwise, the lab data including the COVID-19 screening proved normal. The cerebral CT and MR images, with and without contrast, were interpreted as a giant thrombotic aneurysm extending to the suprasellar region by the emergency radiologist. Also, moderate intraventricular hemorrhage, acute hydrocephalus, and sub-ependymal interstitial edema were observed. Upon further evaluation of the images, the lesion was determined to be an exophytic hemorrhagic hypothalamic mass, and the subsequent biopsy was consistent with prostate cancer metastasis.

Conclusions
The exophytic hemorrhagic hypothalamic metastasis can mimic a ruptured aneurysm on imaging. Given the improved survival of patients with prostate cancer, radiologists may encounter such unusual cerebral metastases from prostate cancers more frequently in the future.
Development and Validation of a Tool Integrating the 21-Gene Recurrence Score and Clinical-Pathological Features to Individualize Prognosis and Prediction of Chemotherapy Benefit in Early Breast Cancer
Authors: Sparano Joseph A. , Crager Michael R. , Tang Gong , Gray Robert J. , Stemmer Salomon M. , Shak Steven 
Published: December 2020

PURPOSEThe 21-gene recurrence score (RS) is prognostic for distant recurrence (DR) and predictive for chemotherapy benefit in early breast cancer, whereas clinical-pathological factors are only prognostic. Integration of genomic and clinical features offers the potential to guide adjuvant chemotherapy use with greater precision.METHODSWe developed a new tool (RSClin) that integrates RS with tumor grade, tumor size, and age using a patient-specific meta-analysis including 10,004 women with hormone receptor–positive, human epidermal growth factor receptor 2–negative, and node-negative breast cancer who received endocrine therapy alone in the B-14 (n = 577) and TAILORx (n = 4,854) trials or plus chemotherapy in TAILORx (n = 4,573). Cox models for RSClin were compared with RS alone and clinical-pathological features alone using likelihood ratio tests. RSClin estimates of DR used a baseline risk with TAILORx event rates to reflect current medical practice. A patient-specific estimator of absolute chemotherapy benefit was computed using individualized relative chemotherapy effect from the randomized TAILORx and B-20 trials. External validation of risk estimation was performed by comparing RSClin estimated risk and observed risk in 1,098 women in the Clalit registry.RESULTSRSClin provides more prognostic information (likelihood ratio χ2) for DR than RS or clinical-pathological factors alone (both P < .001, likelihood ratio test). In external validation, the RSClin risk estimate was prognostic for DR risk in the Clalit registry ( P < .001) and the estimated risk closely approximated the observed 10-year risk (Lin concordance 0.962). The absolute chemotherapy benefit estimate ranges from 0% to 15% as the RS ranges from 11 to 50 using RSClin in a 55-year-old woman with a 1.5-cm intermediate-grade tumor.CONCLUSIONThe RSClin tool integrates clinical-pathological and genomic risk to guide adjuvant chemotherapy in node-negative breast cancer and provides more individualized information than clinical-pathological or genomic data alone.
Rapid Conversion of a Palliative Care Outpatient Clinic to Telehealth
Authors: Lally Kate , Kematick Benjamin S. , Gorman Daniel , Tulsky James 
Published: December 2020

PURPOSE: The coronavirus pandemic has transformed the practice of medicine, forcing a rapid transition to telehealth. As a specialty, palliative care relies upon expert-level communication and interdisciplinary care. We describe the transition of the Dana-Farber Cancer Institute palliative care clinic into a predominantly telemedicine model. RESULTS: We document how we significantly increased goals of care conversations while maintaining patient volume and interdisciplinary care. We present how the components of a palliative visit translate into a virtual model. DISCUSSION: While the transition away from in person visits occurred rapidly, telehealth is likely here to stay. We define the challenges and benefits encountered through increased use of telehealth and identify disparities in healthcare access that will become more pronounced as we move into a communication technology dependent future. We discuss how the pandemic changed the delivery of palliative care in ways that will endure beyond the coronavirus pandemic.
PLEKHG4B enables actin cytoskeletal remodeling during epithelial cell–cell junction formation
Authors: Ninomiya Komaki , Ohta Kai , Yamashita Kazunari , Mizuno Kensaku , Ohashi Kazumasa 
Published: December 2020

ABSTRACT
Cell–cell junction formation requires actin cytoskeletal remodeling. Here, we show that PLEKHG4B, a Rho-guanine nucleotide exchange factor (Rho-GEF), plays a crucial role in epithelial cell–cell junction formation. Knockdown of PLEKHG4B decreased Cdc42 activity and tended to increase RhoA activity in A549 cells. A549 monolayer cells showed ‘closed junctions’ with closely packed actin bundles along the cell–cell contacts, but PLEKHG4B knockdown suppressed closed junction formation, and PLEKHG4B-knockdown cells exhibited ‘open junctions’ with split actin bundles located away from the cell–cell boundary. In Ca2+-switch assays, PLEKHG4B knockdown delayed the conversion of open junctions to closed junctions and β-catenin accumulation at cell–cell junctions. Furthermore, PLEKHG4B knockdown abrogated the reduction in myosin activity normally seen in the later stage of junction formation. The aberrant myosin activation and impairments in closed junction formation in PLEKHG4B-knockdown cells were reverted by ROCK inhibition or LARG/PDZ-RhoGEF knockdown. These results suggest that PLEKHG4B enables actin remodeling during epithelial cell–cell junction maturation, probably by reducing myosin activity in the later stage of junction formation, through suppressing LARG/PDZ-RhoGEF and RhoA–ROCK pathway activities. We also showed that annexin A2 participates in PLEKHG4B localization to cell–cell junctions.
This article has an associated First Person interview with the first author of the paper.
Loot Box Pricing and Design
Authors: Chen Ningyuan , Elmachtoub Adam N. , Hamilton Michael L. , Lei Xiao 
Published: December 2020

In the online video game industry, a significant portion of the revenue is generated from microtransactions, where a small amount of real-world currency is exchanged for virtual items to be used in the game. One popular way to conduct microtransactions is via a loot box, which is a random allocation of virtual items whose contents are not revealed until after purchase. In this work, we consider how to optimally price and design loot boxes from the perspective of a revenue-maximizing video game company and analyze customer surplus under such selling strategies. Our paper provides the first formal treatment of loot boxes, with the aim to provide customers, companies, and regulatory bodies with insights into this popular selling strategy. We consider two types of loot boxes: a traditional one where customers can receive (unwanted) duplicates and a unique one where customers are guaranteed to never receive duplicates. We show that as the number of virtual items grows large, the unique box strategy is asymptotically optimal among all possible strategies, whereas the traditional box strategy only garners 36.7% of the optimal revenue. On the other hand, the unique box strategy leaves almost zero customer surplus, whereas the traditional box strategy leaves positive surplus. Further, when designing traditional and unique loot boxes, we show it is asymptotically optimal to allocate the items uniformly, even when the item valuation distributions are heterogeneous. We also show that, when the seller purposely misrepresents the allocation probabilities, their revenue may increase significantly, and thus, strict regulation is needed. Finally, we show that, even if the seller allows customers to salvage unwanted items, then the customer surplus can only increase by at most 1.4%. This paper was accepted by Victor Martinez-de-Albeniz, operations management.
Modified oblique high tibial osteotomy with minimal fixation for correction of adolescent tibia vara: A prospective case series study
Authors: Aly Ahmad Saeed , Abdelhamid Alsabir Ahmed Refaat , Fahmy Hesham Ahmad , Fayyad Tamer A. 
Published: December 2020

Purpose To assess the reliability and efficacy of the modified oblique high tibial osteotomy for correction of complex deformity in adolescent tibia vara. Methods A total of 19 patients (25 legs) with adolescent tibia vara were enrolled in this study. There were 16 male (84.2%) and three female (15.8%) patients who had modified Rab oblique osteotomy with minimal fixation performed. The age of the patients at time of surgery ranged from 12 years to 30 years (mean 17.23 (sd 5.27)). The body mass index ranged from 22 kg/m2 to 42 kg/m2 (mean 32.05 (sd 6.13)). All patients were followed up for over two years (mean 3.4; 2 to 5). Results The femoro-tibial angle was improved from -34° to -12° (mean -20.04° (sd 5.24°) preoperatively and from -12° to 7°, postoperatively (mean 2.04° (sd 4.07)). Medial deviation of the mechanical axis corrected from 38 mm to 125 mm (mean 76.13 (sd 23.29)) preoperatively to 0 mm to 36 mm (mean 5.74 (sd 7.3)) postoperatively. The time needed to achieve union ranged from eight weeks to 16 weeks (mean 10.2 (sd 2.42)). According to the Lysholm functional knee score scale, there were 15 excellent (78.9%), two good (10.5%), one fair (5.2%) and one poor (5.2%) after correction of the deformity. Conclusion Modified Rab osteotomy with minimal fixation by two or three screws shows promising results with good correction of varus deformity (coronal plane), internal torsion (axial plane) and procurvatum (sagittal plane), in management of adolescent tibia vara with minimal morbidity and complications. Level of evidence IV
Towards vendor-agnostic real-time optical network design with extended Kalman state estimation and recurrent neural network machine learning [Invited]
Authors: Bouda Martin , Krishna Gautam , Krystofik Joe , Oda Shoichiro , Palacharla Paparao 
Published: December 2020

The network operator’s call for open, disaggregated optical networks to accelerate innovation and reduce cost, make progress in the standardization of interfaces, and raise telemetry capabilities in optical network systems has created an opportunity to adopt a new paradigm for optical network design. This new paradigm is driven by direct measurement and continuous learning from the actual optical hardware deployed in the field. We report an approach towards practical, vendor-agnostic, real-time optical network design and network management using a combination of two learning models. We generalize our physics-based optical model parameter estimation algorithm using the extended Kalman state estimation theory and, for the first time, to the best of our knowledge, present results using real optical network field data. An observed 0.3 dB standard deviation of the difference between typical predicted and measured signal quality appears mostly attributable to transponder performance variance. We further propose using the physics-based optical model parameter values as inputs to a second learning model with a recurrent neural network such as a gated recurrent unit (GRU) to allocate the appropriate required optical margin relative to the typical signal quality predicted by the physics-based optical model. A proof of concept shows that for a dataset of 3000 optical connections with a wide variety of amplified spontaneous emission noise and nonlinear noise limited conditions, a 10-hidden-unit 2-layer GRU was sufficient to realize a margin prediction error standard deviation below 0.2 dB. This approach of measurement data-driven automated network design will simplify deployment and enable efficient operation of open optical networks.
Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis A virus isolates from the West Bank, Palestine during the period between 2014 and 2016
Authors: Dumaidi Kamal , Qaraqe Hayah , Al-Jawabreh Amer , Abu-Helu Rasmi , Samarah Fekri , Al-Jawabreh Hanan 
Published: December 2020

BackgroundHepatitis A virus (HAV) infection is one of the major causes of acute viral hepatitis. HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide.AimsThe aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West Bank, Palestine.Study designA cohort of 161 clinically and laboratory-confirmed HAV (IgM-positive) cases and 170 apparently healthy controls from all the districts of the West Bank, Palestine during the period of 2014 to 2016 were tested for HAV infection using IgM antibodies, RT-PCR and sequence analysis of the VP3/VP1 junction region of the HAV genome. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences.ResultsAll the 34 sequences of the HAV were found to be of HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%), but with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h = 8), but low haplotype (gene) diversity (Hd = 0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n = 10) and closer to others haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, infrequent hand washing before meals, and drinking of un-treated water were considered the major HAV risk factors in the present study.ConclusionHaplotype network analysis revealed haplotype variation among the HAV Palestinian sequences despite low genetic variation and nucleotide diversity. In addition, this study reconfirmed that age and parent’s level of education as HAV risk factors, while hand washing and treating drinking water as protective factors.
Segmenting OCT for detecting drug efficacy in CRAO
Authors: Shearer Thomas R. , Hwang Thomas S. , Steinkamp Peter N. , Azuma Mitsuyoshi 
Published: December 2020

Purpose
Thinning of the inner layers of the retina occurs in patients with central retinal artery occlusion (CRAO). The mechanism for such thinning may be partially due to proteolysis by a calcium-activated protease called calpain. Calpain inhibitor SNJ-1945 ameliorated the proteolysis in a past series of model experiments. The purposes of the present retrospective study were to: 1) use segmentation analysis of optical coherence tomography (OCT) images to mathematically model the loss of specific retinal layers in CRAO patients, and 2) predict the number of patients and days of observation needed for clinical trials of inhibitors against CRAO.

Methods
A retrospective case control study was conducted by computer-aided search for CRAO (ICD10 H43.1) with at least one OCT procedure (CPT: 92134) in the OHSU Epic patient data base.

Results
After initial swelling, thinning of the inner retinal layers, especially the ganglion cell (GCL) layer followed exponential decay curves. Using sample size statistics and GCL thickness as a marker in a 30-day clinical trial, 19 eyes/group could theoretically detect a 20% beneficial effect of an inhibitor against CRAO. Other markers, such as the whole retinal thickness and combined inner layers could also be used as less-specific markers.

Conclusions
Using thickness changes in the GCL layer to monitor the efficacy of potential inhibitors against CRAO is practical in human trials requiring a reasonable number of patients and relatively short trial period.

Translational relevance
Measurement of GCL thickness would be a useful indicator of CRAO progression in a clinical trial of putative inhibitors.
Laboratory-confirmed influenza infection and acute myocardial infarction among United States senior Veterans
Authors: Young-Xu Yinong , Smith Jeremy , Mahmud Salaheddin M. , Van Aalst Robertus , Thommes Edward W. , Neupane Nabin , Lee Jason K. H. , Chit Ayman 
Published: December 2020

Background
Previous studies established an association between laboratory-confirmed influenza infection (LCI) and hospitalization for acute myocardial infarction (AMI) but not causality. We aimed to explore the underlying mechanisms by adding biological mediators to an established study design used by earlier studies.

Methods
With data on biomarkers, we used a self-controlled case-series design to evaluate the effect of LCI on hospitalization for AMI among Veterans Health Administration (VHA) patients. We included senior Veterans (age 65 years and older) with LCI between 2010 through 2015. Patient-level data from VHA electronic medical records were used to capture laboratory results, hospitalizations, and baseline patient characteristics. We defined the “risk interval” as the first 7 days after specimen collection and the “control interval” as 1 year before and 1 year after the risk interval. More importantly, using mediation analysis, we examined the role of abnormal white blood cell (WBC) and platelet count in the relationship between LCI and AMI to explore the thrombogenic nature of this association, thus potential causality.

Results
We identified 391 hospitalizations for AMI that occurred within +/-1 year of a positive influenza test, of which 31 (31.1 admissions/week) occurred during the risk interval and 360 (3.5/per week) during the control interval, resulting in an incidence ratio (IR) for AMI admission of 8.89 (95% confidence interval [CI]: 6.16–12.84). In stratified analyses, AMI risk was significantly elevated among patients with high WBC count (IR, 12.43; 95% CI: 6.99–22.10) and high platelet count (IR, 15.89; 95% CI: 3.59–70.41).

Conclusion
We confirmed a significant association between LCI and AMI. The risk was elevated among those with high WBC or platelet count, suggesting a potential role for inflammation and platelet activation in the underlying mechanism.