cssi/SciSciGPT-SciSciNet huggingface dataset:
PTENpred: A Designer Protein Impact Predictor for PTEN-related Disorders.

Abstract Connecting a genotype with a phenotype can provide immediate advantages in the context of modern medicine. Especially useful would be an algorithm for predicting the impact of nonsynonymous single-nucleotide polymorphisms in the gene for PTEN, a protein that is implicated in most human cancers and connected to germline disorders that include autism. We have developed a protein impact predictor, PTENpred, that integrates data from multiple analyses using a support vector machine algorithm. PTENpred can predict phenotypes related to a human PTEN mutation with high accuracy. The output of PTENpred is designed for use by biologists, clinicians, and laymen, and features an interactive display of the three-dimensional structure of PTEN. Using knowledge about the structure of proteins, in general, and the PTEN protein, in particular, enables the prediction of consequences from damage to the human PTEN gene. This algorithm, which can be accessed online, could facilitate the implementation of effective th...
Abstract 5229: Candidate gene analysis of exome sequencing data in smokers susceptible and resistant to chronic obstructive pulmonary disease

Background: Chronic obstructive pulmonary disease (COPD) is a major comorbidity for Lung cancer (LC), the presence of COPD conferring a three- to 10-fold increased risk of LC. Therefore, we employed an extreme-phenotype approach, focused on exome sequencing of 109 susceptibility loci identified in recent genome-wide association studies (GWAS) of LC, COPD, lung function and smoking behavior, to search for COPD disease-causing rare germline mutations. Methods: We selected two extreme categories of smokers from COPDGene: 1) Resistant long-term smokers with normal lung function defined as post-bronchodilator FEV1 ≥ 80% predicted, FEV1/FVC ≥ 0.7, with smoking histories of 15+ pack-years, considered as resistant to the effects of smoking, n = 318; 2) Susceptible smokers with severe COPD defined as GOLD spirometry grades III-IV (post-bronchodilator FEV1 Results: Our analysis revealed two genes with multiple rare non-synonymous substitution variants significantly associated with COPD risk. We identified six rare variants in 10q23.33 Myoferlin (MYOF: p.Arg572Gln, p.Phe1400Leu, p.Tyr1163His, p.Glu1339Lys, p.Leu1582Pro, and p.Arg1630Gln) occurring in 12 susceptible smokers with severe COPD, and three rare variants in 15q15.2 Transglutaminase 5 (TGM5: p.Thr42Asn, Pro136Leu, and p.Val202Ile) occurring in nine susceptible smokers with severe COPD, compared with none of these variants identified in resistant smokers. MAF of these mutations were very rare (range from 0 to 0.003) in the 1000 Genomes and ESP databases. All of these mutations were predicted to be protein damaging and deleterious by bioinformatics algorithms (SIFT, PolyPhen2, Mutation Taster, etc.). We also observed three suggestive rare mutations, 6p21.32 ZBTB9 p.Leu43Val, 9q34.2 DBH p.Gly482Arg, and 10q23.33 IFIT3 p.Leu390Arg, each of which were present in three susceptible smokers and none in resistant smokers. However, we were not able to validate these abovementioned candidate variants in the two replication datasets. This could due to potential false positive results or difference of exome sequencing depth and coverage of the target regions from different platforms. Conclusion: Our results demonstrated potentially disruptive COPD risk-conferring MYOF and TGM5 rare germline mutations that are associated with susceptibility to COPD in one population of smokers, but additional replication of these results in larger populations will be required. Citation Format: Yanhong Liu, Michael H Cho, Dandi Qiao, Farrah Kheradmand, Spiridon Tsavachidis, Georgina Armstrong, Michael Scheurer, David Wheeler, Christopher Amos, Edwin Silverman, Margaret Spitz. Candidate gene analysis of exome sequencing data in smokers susceptible and resistant to chronic obstructive pulmonary disease. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5229.
Insufficient Evidence for Rare Activation of Latent HIV in the Absence of Reservoir-Reducing Interventions.

A priority for HIV cure research is measuring latent infection that can fuel viral recrudescence if patients cease antiretroviral therapy (ART). One important quantity that is difficult to measure is the rate at which latently infected cells activate, giving rise to spreading infection [1]. Pinkevych et al. recently estimated this rate by analyzing several clinical cohorts and concluded that one cell activates every 6 days [2]. This rate is 24-fold lower than our previous estimate of 4 cells/day [1], resulting in far more optimistic predictions for the prospects of reservoir-reducing therapy. We question their estimation approach and suggest that a higher rate is likely for most infected individuals.
Abstract 3854: Inhibition of uracil DNA glycosylase (UDG) sensitizes cancer cells to thymidylate synthase inhibitors

Thymidylate synthase (TS) is responsible for the de novo synthesis of thymine nucleotides that are used as building blocks for DNA synthesis. Two classes of therapeutic agents inhibit TS including fluropyrimidines (eg, 5-FU, 5-FdU) and antifolates (eg, pemetrexed), which lead to depletion of deoxythymidine triphosphate (dTTP) and expansion of deoxyuridine triphosphate (dUTP). Fluropyrimidines are also metabolized to 5-fluorouridine triphosphate (5FdUTP). As a result, both elevated dUTP and 5FdUTP are incorporated into DNA. Uracil DNA N-glycosylase (UDG or UNG) is the primary DNA repair enzyme to remove uracil and 5-FU bases from DNA and creates abasic (AP) sites, thus initiating base excision repair (BER) pathway. However, whether the cytotoxic effects of TS inhibitors are dependent on UDG activity still remains controversial. Previously, our lab has shown that in DLD1 colon cancer cells, knockout of UDG hypersensitized cells to pemetrexed treatment and the cell death was accompanied by remarkable S phase arrest and stalled replication fork. In this study, we examined the cytotoxicity of both pemetrexed and 5-FdU in SW480, HCT116, DLD1, and HEC1A cancer cell lines after performing stable UDG knockdown (KD) by shRNA. We hypothesized that loss of UDG would sensitize cancer cells to TS inhibitors treatment with accumulation of a large amount of uracil and 5-FU bases in DNA and ultimately lead to replication folk collapse. Results showed that reduced UDG protein and activity levels enhanced the cell killing effect, increased the sub-G1 populations, and delayed cell cycle recovery following TS inhibitors treatment. In response to 5-FdU treatment, cells with UDG shRNA were mainly arrested at late G1 and early S phase by 24 hours of treatment. After releasing cells in drug free medium, loss of UDG displayed delayed recovery from cell cycle arrest in comparison to shRNA scramble control cells. We have also detected a significant induction of the amount of AP sites after incubation of extracted DNA from UDG shRNA KD cells with purified UDG protein following 5-FdU treatment, indicating the accumulation of uracil and 5-FU in DNA as a consequence of 5-FdU treatment. Now, further studies are undergoing to determine the actual levels of uracil and 5-FU incorporation into DNA and the replication status after TS inhibitors treatment. These studies confirm that uracil and 5-FU incorporation due to loss of UDG accelerates stall of replication, collapse of the replication fork, and increased cytotoxicity of TS inhibitors. Citation Format: Yan Yan, Allison Condie, Stanton Gerson. Inhibition of uracil DNA glycosylase (UDG) sensitizes cancer cells to thymidylate synthase inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3854. doi:10.1158/1538-7445.AM2015-3854
Jamming mobility in 802.11p networks: Modeling, evaluation, and detection

The development of wireless Vehicular Ad-Hoc Network (VANET) aimed to enhance road's safety and provide comfortable driving environment by delivering early warning and infotainment messages. Intentional jamming attacks target at undermining such a goal by disrupting wireless communications. While detecting jamming attacks is important towards enhancing road safety, it is challenging because VANET operates in outdoor environment (highly changeable road conditions and atmospheric phenomena), and encompasses volatile topology and high mobility of vehicles (traveling speed and directions). To overcome these challenges, in this work, we study jamming attack mobility and behaviors in IEEE802.11p networks. In particular, we focus on analyzing jamming impact based on jammers behaviors, and mobility patterns. Thus, in order to achieve reliable detection, first we identify the impact of vehicles' density on network performance. Then, we study jamming effectiveness when adopting different mobility patterns (stationary, random, or targeting) and behaviors (constant, random, and reactive). Finally, we propose a two phase detection algorithm and evaluate it in a simulation environment. Our approach shows promising results to detect different types of jammers accurately in IEEE802.11p networks.
Reply to Silburt et al.: Concerning sterile inflammation following focused ultrasound and microbubbles in the brain.

We thank Silburt et al. (1) for their comments on our article (2). The authors provide us with an opportunity to expand on sterile inflammation in the brain induced by pulsed focused ultrasound (pFUS) (3). pFUS with microbubbles (MB) resulting in blood–brain barrier disruption (BBBD) is accompanied by plasma protein extravasation into the extracellular space. Fundamentally, any BBBD is a nonhomeostatic condition and leakage of albumin activates microglia and astrocytes (4). To appropriately contextualize our biological data (2), we must make a few technical notes. Silburt et al. (1) accurately point out that many techniques in the FUS field are plagued by lack of rigorous optimization. Accordingly, our study … [↵][1]1To whom correspondence may be addressed. Email: zsofia.kovacs{at}nih.gov or jfrank{at}helix.nih.gov. [1]: #xref-corresp-1-1
DNA Damage and Energy Crisis are Central in the Mechanism for the Cytotoxicity of Pharmacological Ascorbate in Cancer Treatment

The clinical application of ascorbate in cancer treatment has a long and controversial history. The clinical potential of pharmacological ascorbate (P-AscH‒; IV delivery achieving mM concentrations in blood) as an adjuvant in cancer therapy is being re-evaluated. At mM concentrations, P-AscH‒ is thought to exhibit anti-cancer activity via generation of a flux of H2O2 in tumors. However, a complete understanding of mechanism for P-AscH‒ has not yet been established. Here, we use a cell culture model of pancreatic cancer, MIA PaCa-2 and PANC-1, to examine the effects of P-AscH‒ on DNA damage, and downstream consequences, including changes in bioenergetics. We have found that the high flux of H2O2 produced by P-AscH‒ induces both nuclear and mitochondrial DNA damage. In response to this DNA damage, we observed that poly (ADP-ribose) polymerase-1 (PARP-1) is hyperactivated, as determined by increased formation of poly (ADP-ribose) polymer. Using our unique absolute quantitation, we found that the P-AscH‒-mediated the overactivation of PARP-1, which results in consumption of NAD+, and subsequently depletion of ATP (energy crisis) leading to mitotic cell death. Time-course studies with MIA PaCa-2 cells showed that the level of NAD+ and ATP were reduced by 80% immediately after a 1-h exposure to P-AscH‒ (4 mM; 14 pmol cell-1); both species returned to near basal levels within 24 h. In parallel with these metabolic and energetic restorations, the lesions in nuclear DNA were removed within 3 h; however, even after 24 h, lesions in mitochondrial DNA were only partially repaired. We have also found that the ATR-Chk1 pathway has a major role in the maintenance of genomic integrity following treatment with P-AscH‒. Hence, combinations of P-AscH‒ and Chk1 inhibitors could have potential in the treatment of cancer. Hyperactivation of PARP-1 and DNA repair are ATP-consuming processes. Using a Seahorse XF96 Analyzer, we observed no changes in OCR or ECAR/PPR following treatment with P-AscH‒, indicating that the severe decrease in ATP is due solely to increased demand, not changes in the rate of production. These results clearly indicate that the combination of DNA damage coupled with compromised ATP availability could be a key aspect of the anti-cancer activity of P-AscH‒. These preclinical findings can guide the best use of P-AscH‒ as an adjuvant in cancer therapy.
A NEGLECTED WAY OF BEGGING THE QUESTION

I. Q Wjome arguments beg the question. Ques tion-begging arguments are bad arguments and cannot increase the level of justification one has for the conclusion. Question-begging arguments, unlike some other bad arguments, need not suffer the problem of having un justified premises. Even if the premises are justified and even if the premises entail the conclusion, a question-begging argument fails to have any force when it comes to in creasing one's justification for the conclusion. For example, many regard Moore's famous response to skepticism as a question-begging argument:
Routine repeat head CT may not be necessary for patients with mild TBI.

Background Routine repeat cranial CT (RHCT) is standard of care for CT-verified traumatic brain injury (TBI). Despite mixed evidence, those with mild TBI are subject to radiation and expense from serial CT scans. Thus, we investigated the necessity and utility of RHCT for patients with mild TBI. We hypothesized that repeat head CT in these patients would not alter patient care or outcomes. Methods We retrospectively studied patients suffering from mild TBI (Glasgow Coma Scale (GCS) score 13–15) and treated at the R Adams Cowley Shock Trauma Center from November 2014 through January 2015. The primary outcome was the need for surgical intervention. Outcomes were compared using paired Student’s t-test, and stratified by injury on initial CT, GCS change, demographics, and presenting vital signs (mean ± SD). Results Eighty-five patients met inclusion criteria with an average initial GCS score=14.6±0.57. Our center sees about 2800 patients with TBI per year, or about 230 per month. This includes patients with concussions. This sample represents about 30% of patients with TBI seen during the study period. Ten patients required operation (four based on initial CT and others for worsening GCS, headaches, large unresolving injury). There was progression of injury on repeat CT scan in only two patients that required operation, and this accompanied clinical deterioration. The mean brain Abbreviated Injury Scale (AIS) score was 4.8±0.3 for surgical patients on initial CT scan compared with 3.4±0.6 (P Discussion In an environment of increased scrutiny on healthcare expenditures, it is necessary to question dogma and eliminate unnecessary cost. Our data questions the use of routine repeat head CT scans in every patient with anatomic TBI and suggests that clinically stable patients with small injury can simply be followed clinically. Level of evidence Level III.
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.

ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html .
Does intrinsic reward motivate cognitive control? a naturalistic-fMRI study based on the synchronization theory of flow

Cognitive control is a framework for understanding the neuropsychological processes that underlie the successful completion of everyday tasks. Only recently has research in this area investigated motivational contributions to control allocation. An important gap in our understanding is the way in which intrinsic rewards associated with a task motivate the sustained allocation of control. To address this issue, we draw on flow theory, which predicts that a balance between task difficulty and individual ability results in the highest levels of intrinsic reward. In three behavioral and one functional magnetic resonance imaging studies, we used a naturalistic and open-source video game stimulus to show that changes in the balance between task difficulty and an individual's ability to perform the task resulted in different levels of intrinsic reward, which is associated with different brain states. Specifically, psychophysiological interaction analyses show that high levels of intrinsic reward associated with a balance between task difficulty and individual ability are associated with increased functional connectivity between key structures within cognitive control and reward networks. By comparison, a mismatch between task difficulty and individual ability is associated with lower levels of intrinsic reward and corresponds to increased activity within the default mode network. These results suggest that intrinsic reward motivates cognitive control allocation.
Development of spacecraft radiated susceptibility RS103 requirements from modeling methods

In defining radiated susceptibility requirements for a spacecraft with multiple number of receivers and transmitters in close proximity to each other, the main objective of an RF coupling analysis is to determine if the mechanical configuration of the receiver and transmitter antennas presents a risk to the functionality and safety of sensitive science instruments on the payload as a result of unintended RF coupling. Where there is a potential risk for interference or permanent damage, further analysis is required to evaluate the feasibility of mitigation schemes, such as mechanical reconfiguration of antennas or additional RF filtering. From these coupling analysis results, radiated susceptibility RS103 requirements are derived to better reflect actual requirement levels with adequate test margins.
Nonlinear elastic analysis of adhesive blister test

A nonlinear elastic analysis of a blister test is conducted for rubber-like material described by the Ogden-Tschoegl strain energy function. A finite element program is applied to the analysis which is formulated based on the total Lagrangian procedure and capable of treating deformation-dependent pressure loading problems. The dependence of specific adhesive fracture energy γa on critical pressure pcris analyzed for a blister test specimen with different geometry and different material constants. It is suggested that the unbonded radius a in the dimensionless representation p cr 2 a/Eγa should be replaced by an average value ā in the numerical analysis. The numerical analysis of the blister test is also discussed in general.
The Minipig as a Model for the Study of Aging in Humans

Both age and sex have been shown to affect lipid and carbohydrate metabolism in animals and humans. There is a gradual loss of glucose homeostasis and concomitant increase in insulin resistance with age. Carbohydrate and lipid metabolism in different metabolic conditions including obesity and noninsulin dependent diabetes mellitus (NIDDM), both of which are age dependent, are controlled by pancreatic, pituitary and adrenal hormones. Therefore, we assessed age related changes in plasma hormones in male and female Hormel miniature swine. Animals were fed an energy restricted cholesterol free, low fat stock diet postweaning. Animals were sacrificed at various ages, ranging from prepubertal, 10 years. Levels of insulin, glucagon, adrenocorticotropic hormone (ACTH), Cortisol and androstenedione were measured by radioimmunoassay in plasma from both sexes. In addition, dehydroepiandrosterone-sulfate (DHEA-S), aldosterone and testosterone were measured in male swine. No effect of age nor sex was observed on plasma insulin and ACTH levels though an interaction was observed between age and sex for ACTH. Thus, with age, levels of ACTH tended to increase in males but decrease in females. Plasma glucagon was higher in males than females and showed age dependent increases in males but not in females. Plasma androstenedione was 3 to 5 fold higher in males than in females and the level was lower in mature male swine than either prepubertal or older swine. There were sex and age dependent changes in plasma Cortisol levels with an increase with age in males and a decrease with age in females. There were no age dependent changes in plasma DHEA-S and aldosterone levels in the males. Plasma testosterone levels were higher in prepubertal swine than in mature or older animals. In swine, both age and sex affect hormonal changes, which then impact on metabolic parameters controlled by hormones, notably carbohydrate and lipid metabolism. Energy restriction appears to have a beneficial effect in retarding the aging process and miniature swine can be used as a model for the study of aging in humans.
Titanium-chromium phase diagram

An investigation of the Ti-Cr system has shown the presence of a complete series of solid solutions in the s phase, with a minimum in the solidus near 50 pct Cr. An intermetallic compound, TiCr2, forms during cooling from the s solid solution. There is a eutectoid reaction at the low chromium side of the system.
Clowder: Open Source Data Management for Long Tail Data

Clowder is an open source data management system to support data curation of long tail data and metadata across multiple research domains and diverse data types. Institutions and labs can install and customize their own instance of the framework on local hardware or on remote cloud computing resources to provide a shared service to distributed communities of researchers. Data can be ingested directly from instruments or manually uploaded by users and then shared with remote collaborators using a web front end. We discuss some of the challenges encountered in designing and developing a system that can be easily adapted to different scientific areas including digital preservation, geoscience, material science, medicine, social science, cultural heritage and the arts. Some of these challenges include support for large amounts of data, horizontal scaling of domain specific preprocessing algorithms, ability to provide new data visualizations in the web browser, a comprehensive Web service API for automatic data ingestion and curation, a suite of social annotation and metadata management features to support data annotation by communities of users and algorithms, and a web based front-end to interact with code running on heterogeneous clusters, including HPC resources.
Tunable Band Topology in Gyroscopic Lattices

Gyroscopic metamaterials, mechanical structures composed of interacting spinning tops, have recently been found to support one-way topological edge waves. In these structures, the time-reversal symmetry breaking that enables their topological behavior emerges directly from the lattice geometry. Here we show that variations in the lattice geometry can give rise to more complex band topology than has been previously described. A “spindle” lattice (or truncated hexagonal tiling) of gyroscopes possesses both clockwise and counterclockwise edge modes distributed across several band gaps. Tuning the interaction strength or twisting the lattice structure along a Guest mode opens and closes these gaps and yields bands with Chern numbers of |C| > 1 without introducing next-nearest-neighbor interactions or staggered potentials. A deformable honeycomb structure provides a simple model for understanding the role of lattice geometry in constraining the effects of time-reversal symmetry and inversion symmetry breaking. Last, we find that topological band structure generically arises in gyroscopic networks, and a simple protocol generates lattices with topological excitations.
Water Entry of Cylindrical Shells: Theory and Experiments

Modeling hydroelastic response of lightweight structures to water impact plays a pivotal role in the design of lightweight marine vessels and crew capsules. In contrast to the majority of studies t...
Abstract WMP55: Increased Risk of Acute Ischemic Stroke in Multiple Sclerosis: Analysis of a Large National Cohort

Background: The advent of mechanical thrombectomy in acute stroke care has reignited interest in the arena of neuro-inflammation and neuro-plasticity to optimize stroke management and further impro...
Depression and health care utilization and costs in patients diagnosed with cancer.

e23128Background: The aims of this study were to examine the associations between depression and complications, health care utilization and costs in patients with cancer. Methods: Patients diagnose...
An Integral Form of the Nonlinear Schrödinger Equation with Variable Coefficients

We discuss an integral form of the Cauchy initial value problem for the nonlinear Schrodinger equation with variable coefficients. Some special and limiting cases are outlined. For the linear case the inverse of the time evolution operators and estimates in the supremum norm are established.
Differentiation and Integration

Differentiation and integration procedures are described for discrete data. The procedures are completely different for the two methods and there are different possible complications.
Bilateral acute retinal necrosis caused by two separate viral etiologies.

Abstract Purpose To describe an unusual case of bilateral acute retinal necrosis (ARN) that was caused by varicella zoster virus in one eye and Epstein-Barr virus in the fellow eye. Observations A 67-year-old immunocompromised man presented with ARN in the left eye following a dermatomal vesicular rash, with an aqueous sample positive for varicella zoster virus. Four months later, the patient presented with panuveitis and serous retinal detachment in the right eye, with vitreous sample positive for Epstein-Barr virus and negative for varicella zoster, herpes simplex, and cytomegalovirus. Conclusions and importance We report a rare case of bilateral ARN with independent infection of each eye by different viruses; varicella zoster in the left eye and, four months later, Epstein-Barr virus in the right eye. Immunocompromised patients are vulnerable to ARN from any of its inciting viral causes, and intraocular fluid should be obtained for diagnostic confirmation from the second eye in cases of bilateral ARN.
Effects of Tourniquets in the Development of Pain States: a Novel Clinical Pilot Study and Review of Utilization of Tissue Oximetry to Measure Neural Ischemia

Approximately 20% of patients undergoing surgery develop persistent lower extremity pain following total knee arthroplasty. Animal studies have confirmed that prolonged tourniquet time increases the risk of endoneural ischemia and can mediate or modulate the development of chronic pain. The use of Near InfraRed Spectroscopy (NIRS) adjacent to nerve tissue, previously described as ONG has been shown to detect early neural compromise and has demonstrated clinical utility in carpal tunnel diagnosis. In this pilot study, we recruited 10 healthy adult volunteers to undergo oxyneurography (ONG) and sensory nerve conduction testing (sNCT). We performed testing on the upper and lower extremities in each individual. The tourniquet was applied followed by measurements of sNCT and ONG as described. We observed a significant drop in the mean ONG index at 3 and 5 min following tourniquet inflation in upper and lower extremities. Similar to raw ONG values, there was significant variability in sNCT measurements, which in general increased from baseline with tourniquet inflation. In the upper extremity, there was a significant increase in sNCT with tourniquet inflation, while in the lower extremity, there was a trend towards significance. The use of ONG can be supported as a diagnostic tool to detect nerve ischemia and to potentially reduce the incidence of tourniquet-mediated or -modulated neural ischemia and reduce the development of chronic post-tourniquet pain.
Lessons Learned in Leaving the Library and Coming Back Again

In early March 2020, libraries across the Commonwealth of Pennsylvania began to close in the wake of the COVID-19 crisis. On March 19, staff members in the Interlibrary Loan (ILL) Department at Penn State University Libraries pivoted to providing remote services to Penn State users and library partners from around the world. In addition to describing the difficulties of transitioning to and the realities of working from home, this piece describes the challenges experienced in returning to the library. Considerations for the future are also discussed.
Reverberation Noise Suppression in Ultrasound Channel Signals Using a 3D Fully Convolutional Neural Network

Diffuse reverberation is ultrasound image noise caused by multiple reflections of the transmitted pulse before returning to the transducer, which degrades image quality and impedes the estimation of displacement or flow in techniques such as elastography and Doppler imaging. Diffuse reverberation appears as spatially incoherent noise in the channel signals, where it also degrades the performance of adaptive beamforming methods, sound speed estimation, and methods that require measurements from channel signals. In this paper, we propose a custom 3D fully convolutional neural network (3DCNN) to reduce diffuse reverberation noise in the channel signals. The 3DCNN was trained with channel signals from simulations of random targets that include models of reverberation and thermal noise. It was then evaluated both on phantom and in-vivo experimental data. The 3DCNN showed improvements in image quality metrics such as generalized contrast to noise ratio (GCNR), lag one coherence (LOC) contrast-to-noise ratio (CNR) and contrast for anechoic regions in both phantom and in-vivo experiments. Visually, the contrast of anechoic regions was greatly improved. The CNR was improved in some cases, however the 3DCNN appears to strongly remove uncorrelated and low amplitude signal. In images of in-vivo carotid artery and thyroid, the 3DCNN was compared to short-lag spatial coherence (SLSC) imaging and spatial prediction filtering (FXPF) and demonstrated improved contrast, GCNR, and LOC, while FXPF only improved contrast and SLSC only improved CNR.
Can a Connection with the Past Influence Environmental Concern and Attitude toward Slow Fashion

We investigated how (i) consumers' connection with indigenous cultural values influences their environmental concern and attitude toward slow fashion; (ii) environmental concern influences attitude toward slow fashion and; (iii) if the environmental concern mediates the relationship between connection with indigenous cultural values and attitude toward slow fashion. We conducted an online survey with a national sample of millennials of the U.S. (n = 300). We filled some important gaps in the literature by providing empirical evidence that the (i) connection with indigenous cultural values positively influences environmental concern and the attitude toward slow fashion; (ii) environmental concern mediates the relationship between connection with indigenous cultural values and the attitude toward slow fashion. Therefore, while a high environmental concern can translate into a positive attitude toward slow fashion, connection with indigenous cultural values forms an important variable that can further foster the positive attitude toward slow fashion.
Assessing the Utility of In-Line Intravenous Infusion Filters.

Abstract The use of in-line filters to remove fibrous material in the administration of intravenous fluids dates to the early 1830’s. Following advancements in therapeutic interventions, high volume fluid support and parenterally administered drugs and biologic preparations, some observers are calling for a routine use of bedside filtration. Unfortunately, the assessment of filter components, their interaction and compatibility with the drug product, and the impact of use on clinical outcomes cannot be conducted by a single entity. Recommendations for use are often predicated upon fragmented and incomplete information. The current challenges in evaluating the benefit/risk profile for the use of in-line filters should not be ignored. While there are select instances showing well-defined therapeutic settings where in-line filtration of intravenous infusions would likely provide an additional safety margin and hence, net benefit, the majority of observational studies to date fail to provide sufficient scientific support for broad-based routine use. While infusion set filters are appropriate where expert opinion is well corroborated by scientific evidence, the general and routine use of filters used during parenteral administration cannot be supported by substantive studies and should not be routinely utilized. Ultimately, the determination falls to a healthcare provider with the information available at-hand.
Physics informed neural network for parameter identification and boundary force estimation of compliant and biomechanical systems

This paper presents the framework of a physics-informed neural network (PINN) with a boundary condition-embedded approximation function (BCAF) for solving common problems encountered in flexible mechatronics and soft robotics; both forward and inverse problems are considered. Unlike conventional PINNs that minimize a lumped loss function including the errors contributed by the initial or boundary conditions (ICs or BCs), the BCAF-PINN completely satisfies the ICs and/or BCs while minimizing a loss function for parameter identification and boundary force estimation, overcoming a common erroneous-convergence problem due to unbalanced gradients in training a PINN. The formulation and implementation of a BCAF-PINN are illustrated with three practical applications, including a nonlinear system where solutions are available for numerical verification and for comparing with conventional PINNs, and a biomechanical system where a BCAF-PINN uses multiple cycles of natural foot flexion to identify its dynamic parameters experimentally. While overcoming several problems associated with traditional studies based on perturbation models with certain level of muscle contraction, the damping ratio identified by the BCAF-PINN indicates that the ankle joint is an overdamped system during flexion, consistent with that observed in published experiments.
Do southern seed or soil microbes mitigate the effects of warming on establishing prairie plant communities

Restoration in this era of climate change comes with a new challenge: anticipating how best to restore populations to persist under future climate conditions. Specifically, it remains unknown whether locally adapted or warm-adapted seeds best promote native plant community restoration in the warmer conditions predicted in the future and whether local or warm-adapted soil microbial communities could mitigate plant responses to warming. This may be especially relevant for biomes spanning large climatic gradients, such as the North American tallgrass prairie. Here, we used a short-term mesocosm experiment to evaluate how seed provenances (Local Northern region, Non-local Northern region, Non-local Southern region) of 10 native tallgrass prairie plants (four forbs, two legumes, and four grasses) responded to warmer conditions predicted in the future and how soil microbial communities from those three regions influenced these responses. Warming and seed provenance affected plant community composition and warming decreased plant diversity for all three seed provenances. Plant species varied in their individual responses to warming, and across species, we detected no consistent differences among the three provenances in terms of biomass response to warming and few strong effects of soil provenance. Our work provides evidence that warming, in part, may reduce plant diversity and affect restored prairie composition. Because the southern provenance did not consistently outperform others under warming and we found little support for the "local is best" paradigm currently dominating restoration practice, identifying appropriate seed provenances to promote restoration success both now and in future warmer environments may be challenging. Due to the idiosyncratic responses across species, we recommend that land managers compare seeds from different regions for each species to determine which seed provenance performs best under warming and in restoration for tallgrass prairies.
Meeting Individual Needs of Gifted Learners: A Holistic Approach

There is a certain anticipation that arises when opening a text with the artwork of a child on the cover. Clearly, the author relishes and values the spirit of the child and invites the reader to d...
Bacterial expression, purification, and functional mapping of the amyloid beta/A4 protein precursor.

The secreted form of Alzheimer amyloid beta/A4 protein precursor (APP) has been shown to be involved in cell growth regulation (Saitoh, T., Sundsmo, M., Roch, J.-M., Kimura, N., Cole, G., Schubert, D., Oltersdorf, T., and Schenk, D.B. (1989) Cell 58, 615-622). Using a strong prokaryotic expression system, we expressed, in Escherichia coli, peptide fragments covering different regions of the secreted form of APP-695. The longest of these fragments (KB75, 572 amino acids from Val-20 to Ile-591), which contained neither the Kunitz-type protease inhibitor (KPI) domain nor the amyloid beta/A4-protein domain, was purified and shown to be biologically active in terms of growth regulation. Two other APP fragments (KB48, 316 amino acids from Val-20 to Met-335; and RB17, 150 amino acids from Thr-296 to Pro-445), overlapping by only 40 amino acids at a close site C-terminal to the KPI insertion site, were also active. Furthermore, a chemically synthesized 40-residue peptide corresponding to this region of overlap also stimulated the growth of A-1 fibroblasts. These results establish the presence of growth-promoting activity in the secreted form of APP-695 and suggest that the site of this activity of APP-695 lies within a 40-amino acid domain next to the KPI insertion site.
Interplanetary space-A new laboratory for rarefied gas dynamics

Interplanetary space provides simultaneously the best vacuum available to man and, because of the solar wind, a tenuous and unsteady high-speed outflow of predominantly hydrogen gas from the sun, a remarkable variety of rarefied gasdynamics phenomena, to observe. A review is provided of these phenomena, and of the way in which the present level of understanding has been achieved.
Personalizing annual lung cancer screening for patients with chronic obstructive pulmonary disease: A decision analysis.

Background Lung cancer screening with annual chest CT is recommended for current and former smokers with ≥30+ pack-year smoking history. Patients with chronic obstructive pulmonary disease (COPD) are at increased risk of developing lung cancer and may benefit from screening at lower pack-year thresholds.
Microfinance : a reader

1. An Introduction to Microfinance 2. Microfinancial Services and Poor People 3. Microfinance and Poverty Reduction 4. Microfinance, Gender and Social Development 5. Microfinance: Innovations in Product Delivery 6. Microinsurance 7. Regulating and Supervising Microfinance Institutions 8. Impact Assessment of Microfinance 9. The Future of Microfinance
Extracorporeal membrane oxygenation trials

The randomized trial reported by O9Rourke and coworkers1 (they call it a randomized study but why not call it what it is?) provides insight into the dilemma faced when trying to evaluate a therapy believed, rightly or wrongly, to be efficacious. The fact that extracorporeal membrane oxygenation therapy for persistent pulmonary hypertension of the newborn was introduced in 1976 but not tested in a trial until years later, and then only after it was already viewed in many quarters as effective, is a sad comment on how therapies are introduced and accepted into the armamentarium of treatments.2,3
Pneumothorax in the newborn: clinical presentation, risk factors and outcomes

AbstractObjective: We aimed to compare clinical presentation and risk factors associated with the development of pneumothorax among newborns of different birth weight (BW) categories.Methods: We collected clinical and respiratory data on all newborns diagnosed with pneumothorax over a 10-year period. Infants were classified into two groups with BW ≥2500 g and <2500 g.Results: From 13 811 infants, we identified 77 with pneumothorax (BW ≥2500 g in 33 and BW <2500 g in 44 infants). The prevalence of pneumothorax in the two BW categories was 0.27% and 2.5%, respectively. Infants with BW ≥2500 g were diagnosed with neumothorax at a median age of 5.5 h, and mostly (70%) did not require intubation. Infants with BW <2500 g were diagnosed with pneumothorax at a median age of 34 h, presenting with hypercarbia and increased requirement for supplemental oxygen. The majority of these infants (89%) received mechanical ventilation after pneumothorax. When compared to matched controls, there was a lower proportion of Afr...
High-temperature absorption coefficient of methane at 3.392μ

Abstract The spectral absorption coefficient of methane at 3.392μ has been measured in the temperature range 965 ⩽ T , °K≤2710 behind incident and reflected shock waves. It is given by the relation P '= P ' 0 ( T 0 / T ) n where P ' 0 =(1.34±0.58)x10 2 cm -1 atm -1 at T 0 =300°K and n =2.88±0.21. The empirically determined temperature exponent n may be approximately accounted for by a simplified theoretical analysis.
Experimental Evaluation of the Travenol and Landé-Edwards Membrane Oxygenators for Use in Neonate Perfusions

Abstract A compact, low-prime cardiopulmonary bypass circuit which employs a membrane oxygenator has recently been developed for use in neonatal perfusions. In order to assess the comparative performance of the Travenol and Lande-Edwards membrane oxygenators when used in this circuit, two groups of 6 puppies each weighing between 4 and 6 kg. underwent one hour of total bypass with each unit using a 50% blood–50% Normosol prime. The Lande-Edwards oxygenator required a thorough rinsing prior to use in order to perform effectively, while the Travenol membrane oxygenator could be used as packaged. Five of the 6 puppies in each group were long-term survivors. Adequate oxygenation, CO 2 exchange (pO 2 > 200 mm. Hg, pCO 2 2 > 25 mm. Hg) together with low hemolysis (plasma hemoglobin
Prognostic factors for disease-specific survival after first relapse of soft-tissue sarcoma: analysis of 402 patients with disease relapse after initial conservative surgery and radiotherapy.

Abstract Purpose To document the prognostic factors for survival of patients with soft-tissue sarcoma sustaining a first relapse after definitive treatment. Methods and materials The clinicopathologic features, relapse patterns, and disease-specific survival rates for 402 consecutive patients sustaining a first relapse of sarcoma after combined surgery and radiotherapy were retrospectively reviewed. Factors affecting disease-specific survival after relapse were evaluated with univariate and multivariate techniques. Results The median follow-up after relapse was 6.8 years. The overall disease-specific survival rate was 25%, 19%, and 16% at 5, 10, and 15 years, respectively, after the first relapse. The median survival duration was 21 months. Patients with an isolated local recurrence had a 5- and 10-year disease-specific survival rate of 48% and 46%, respectively, and those with an initial metastatic relapse had a disease-specific survival rate of 16% and 10%, respectively (p 12 vs. ≤12 months); and initial tumor size (≤5 vs. >5 cm). Although the development of subsequent metastasis was the major cause of death, a significant fraction of patients died of uncontrolled primary tumor. For patients presenting with metastasis as the first relapse, the time to metastasis was the major determinant of survival (>12 vs. ≤12 months). Long-term salvage was largely confined to patients who could and did undergo resection of relapsed disease, either local or metastatic. Conclusion On the whole, patients whose sarcoma relapses fare poorly. However, select subgroups are potentially salvageable. Patients with an isolated local recurrence at sites other than the head and neck and deep trunk have a reasonable prospect for satisfactory outcome. Surgical resection of recurrences and metastases appears to play a major role in potential salvage.
Platelet spherocytosis: a new bleeding disorder.

The present study evaluated a child with thrombocytopenia and a rare congenital bleeding disorder associated with platelet spherocytosis. Differential interference phase contrast microscopy (DIC) revealed that his platelets were spherical in form. Examination of thin sections in the electron microscope showed that his platelets were nearly devoid of microtubules (MT) and microtubule coils (MTC) that support the discoid shape in 100% of normal platelets. Immunofluorescence with a monoclonal antibody to tubulin, the precursor protein of MT, revealed bright rings in normal cells and diffuse fluorescence of patient platelets. The brightness of the fluorescence emitted by patient platelets was comparable to the diffuse fluorescence of normal platelets after chilling to dissolve intact MT, suggesting normal and patient cells contained comparable amounts of tubulin. Exposure of patient platelets to Taxol, an agent that stabilizes and induces MT, caused MT formation in 82% of patient platelets and MTC development in 11%, resulting in their conversion to discs. Glycoproteins GPIIb/IIIa and GPIb were present on patient platelets, and the cells contained normal numbers of dense bodies, ruling out storage pool disease. The patient's platelets adhered to and spread normally on glass but failed to undergo rapid, irreversible aggregation when stirred with agents that produced a complete response in normal discoid platelets, even when the patient's platelets were concentrated. The poor response of spherical platelets was associated with failure to become irregular and extend long filopodia. Thus, the spherical shape of patient platelets may contribute to the thrombocytopenia and to the clinical bleeding symptoms.