gebhart/patrepeval huggingface dataset:
The effect of moderate intensity aerobic exercise training on general anxiety severity in young adults (2018)

Anxiety disorders are highly debilitating mental illnesses. They are characterized by heightened worry and physiological arousal that manifest as psychological, physiological, and behavioral disturbances. Critically, a large proportion of the population suffers from elevated anxiety. Although physical exercise has been proposed as a potential treatment for managing anxiety symptoms, the strength of this effect may vary depending on the anxiety severity of the sample at intervention onset. The present study examined the effect of moderate intensity aerobic exercise training on anxiety in young adults. We hypothesized that anxiety would be significantly lower after nine weeks of exercise training compared to no exercise training, and that this effect would be moderated by anxiety severity. Fifty-five inactive participants (47 females) were randomized into either an exercise group or a non-exercise control group. The exercise group completed three moderate intensity continuous aerobic exercise sessions per week for nine weeks, whereas the control group remained inactive. Anxiety was measured before and after the intervention using the Beck Anxiety Inventory. At the end of the intervention, the exercise group had significantly lower anxiety than the control group (p = .016). This effect was moderated by anxiety severity, such that the effect of exercise on post-intervention anxiety was only observed in individuals with high levels of anxiety at baseline [B = -10.60, SE = 3.48, p = .0037, CI = -17.59 to -3.60]. These findings point to regular aerobic exercise as an effective tool for young adults experiencing elevated anxiety to manage their symptoms.
Shiny-Seq: advanced guided transcriptome analysis (2019)

Abstract Objective Over the last years, Next Generation Sequencing has generated huge amounts of gene expression data supporting research to answer biological and medical questions. While several tools and advanced guided analysis pipelines were designed for this purpose, some require programming skills and others lack the support for many important features that enable more comprehensive data analysis. Results We present the tool Shiny-Seq. It has many new features such as batch effect evaluation and removal, quality check with several visualization options, enrichment analysis with multiple biological databases, identification of patterns using advanced methods such as weighted gene co-expression network analysis, summarizing analysis as power point presentation and all results as tables via one click feature. The source code is published on GitHub (https://github.com/schultzelab/Shiny-Seq) with the code licensed under GPLv3. Shiny-Seq is written in R using the Shiny framework. In addition, the application is hosted on a public website hosted by shinyapps.io server (https://schultzelab.shinyapps.io/Shiny-Seq/) and as a Docker image https://hub.docker.com/r/makaho/shiny-seq.
Clinical grade adult stem cell banking (2009)

There has been a great deal of scientific interest recently generated by the potential therapeutic applications of adult stem cells in human care but there are several challenges regarding quality and safety in clinical applications and a number of these challenges relate to the processing and banking of these cells ex-vivo. As the number of clinical trials and the variety of adult cells used in regenerative therapy increases, safety remains a primary concern. This has inspired many nations to formulate guidelines and standards for the quality of stem cell collection, processing, testing, banking, packaging and distribution. Clinically applicable cryopreservation and banking of adult stem cells offers unique opportunities to advance the potential uses and widespread implementation of these cells in clinical applications. Most current cryopreservation protocols include animal serum proteins and potentially toxic cryoprotectant additives (CPAs) that prevent direct use of these cells in human therapeutic applications. Long term cryopreservation of adult stem cells under good manufacturing conditions using animal product free solutions is critical to the widespread clinical implementation of ex-vivo adult stem cell therapies. Furthermore, to avoid any potential cryoprotectant related complications, reduced CPA concentrations and efficient post-thaw washing to remove CPA are also desirable. The present review focuses on the current strategies and important aspects of adult stem cell banking for clinical applications. These include current good manufacturing practices (cGMPs), animal protein free freezing solutions, cryoprotectants, freezing & thawing protocols, viability assays, packaging and distribution. The importance and benefits of banking clinical grade adult stem cells are also discussed.
An AAVP-based solid-phase transducing matrix for transgene delivery: potential for translational applications (2017)

A hybrid vector of adeno-associated virus and phage (termed AAVP) has been introduced as a platform for systemic ligand-directed delivery of transgenes to tumors over the past decade. A series of studies have evaluated the AAVP platform for potential theranostic or purely therapeutic applications in several tumor models. Sufficient ligand-directed tumor targeting consistently resulted in specific molecular-genetic imaging and/or anti-tumor responses to 'suicide' transgene delivery. However, efforts to optimize transduction efficiency are still ongoing. Here, we set out to expand the translational utility of AAVP by combining it with gold (Au) nanoparticles in order to generate a 'transducing matrix' for improved targeted gene delivery in solid phase. Targeted AAVP-based solid-phase transduction is superior to conventional transduction in soluble (aqueous) environments. This transducing matrix is stable and can be further modified with additional attributes (for example, magnetization) for targeted imaging and therapeutic gene delivery. Notably, it spontaneously assembles around cells in vitro to markedly enhance transduction capabilities compared with AAVP alone. This versatile nanoplatform may enable new applications of AAVP for transgene delivery in translational settings including, for example, efforts toward complex tissue patterning.
Dantrolene reverses the increase in intracellular Ca2+ associated with exertional rhabdomyolysis in human skeletal muscle. (1996)

Clinical Pharmacology & Therapeutics (1996) 59, 187–187; doi: 10.1038/sj.clpt.1996.247
PROPYLENE GLYCOL RELEASES CALCIUM FROM MITOCHONDRIAL STORES IN RAT CEREBROCORTICAL SYNAPTOSOMES (2004)

In Ca2+-free medium, propylene glycol (PG) increases the cytosolic-free Ca2+ concentration ([Ca2+]i) in rat cerebrocortical synaptosomes. In the current studies, the authors investigated the intracellular source of this Ca2+. PG (0.5-5% v/v) dose-dependently increased [Ca2+]i in Ca2+-free medium. The increase in [Ca2+]i was completely inhibited by pretreatment with the mitochondrial uncoupler, carbonylcyanide m-chlorophenylhydrazone (CCCP, 10 microM). The inhibitory effect of CCCP was dependent on the concentration and the pretreatment time. These results suggest that, in Ca2+-free medium, PG increases [Ca2+]i in rat cerebrocortical synaptosomes by releasing Ca2+ from mitochondrial stores.
Stress-Mediated Attenuation of Translation Undermines T Cell Tumor Control (2022)

Abstract Protein synthesis enables cell growth and survival, but the molecular mechanisms through which T cells suppress or maintain protein translation in the stress of solid tumors are unknown. Using mouse models and human tumors we demonstrate that protein translation in T cells is repressed by the solid tumor microenvironment (TME) due to activation of the unfolded protein response (UPR) via phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (p-eIF2α). Given that acute glucose deprivation in T cells exacerbated p-eIF2α, we show that metabolic reprogramming toward glycolytic independence allays the UPR and p-eIF2α, enabling sustained protein translation in T cells in TME stress. UPR mitigation was associated with enhanced degradation of proteins in antitumor T cells, as proteasome inhibition resulted in eIF2α phosphorylation, attenuation of translation, and loss of antitumor efficacy. In contrast, proteasome stimulation relieved translation inhibition, inducing robust T cell tumor control, offering a new therapeutic avenue to fuel the efficacy of tumor immunotherapy.
Environment for multiprocessor simulator development (2002)

Performance estimation is essential for designing and investigating new architectures including multiprocessors. Software simulation is one of the most common methods, since there is no limitation on device technology nor hardware configuration. Although lots of software simulators have been developed and used, they must be modified for each distinct target system. For designers of new architectures, it is often a cumbersome job. ISIS, an architecture independent simulation kit for multiprocessors, is developed so as to reduce such designers load. It includes various small simulators called "Units" corresponding to processors, buses, memories, caches and I/O devices. ISIS users can build simulators for their original target architectures only by connecting "Units" each other. The implementation cost is much reduced with little runtime overhead. A sample instruction-level multiprocessor simulator which has 4 processors can be executed 40000 to 70000 steps per second. This paper also reports experimental results of ISIS in various research projects.
Phosphorus Loss in Runoff from Long‐term Continuous Wheat Fertility Trials (2005)

Some wheat ( Triticum aestivum L.) farmers in the southern Great Plains routinely apply P fertilizer without soil testing. This practice may lead to P buildup in soils, hence, increased P runoff potential, making soil P management of concern in continuous wheat production. At present, there is also debate over the nature of P loss trends, particularly whether soil P release to runoff can be described generally, across a broad range of soils, or is soil‐specific. Paired 1 m by 2 m runoff plots were established on three existing long‐term continuous winter wheat fertility experiments. Two experiments have received annual fertilizer P application at different rates since 1970 (0–44 kg P ha −1 ), and the third received a one‐time P application at much higher rates in 1977 (0–587 kg P ha −1 ). Rainfall‐runoff experiments were conducted following the National P Research Project protocol. Simulated rain (75 mm h −1 ) produced 30 min of runoff from plots with different soil test P levels. Soil Mehlich‐3 P (M3P) ranged from 11.5 to 130 mg kg −1 and water‐soluble P (WSP) ranged from 0.70 to 15.7 mg kg −1 Runoff total P and dissolved reactive P (DRP) concentrations ranged from 0.47 to 1.5 and 0.03 to 0.70 mg L −1 , respectively. Dissolved reactive P in runoff was significantly related to M3P, WSP, and ammonium oxalate P saturation index (PSI ox ) for combined soils as well as for individual soil series. Significant differences ( p &lt; 0.05) among the slopes of the regressions for the DRP‐M3P, DRP‐WSP, and DRP‐PSI ox relationships indicate that the relationships are soil specific. This study highlights the need for soil specific management to protect water quality.
Limitations of power-spectrum and time-domain analysis of heart rate variability in short-term ECG recorded using telemetry in unrestrained rats (2003)

A radio-telemetry technique used to record electrophysiological signals in animals is broadly used in experimental studies. Using implantable probes, this technique can record electrocardiographic (ECG) signals without disturbing animal activities. In this study, we investigated the stability of heart rate variability (HRV) parameters computed from radio-telemetry ECG recordings in unrestrained rats. The experiment involved 4 normal rats in which ECGs were recorded during baseline conditions with and without drug-induced autonomic blockade. The study revealed that the stability of HRV estimators for both time and frequency domain analysis in unrestrained rats was highly dependent on the average heart rate (related to physical rats activity) as well as the length of the ECG recording.
Resistor-logic demultiplexers for nanoelectronics based on constant-weight codes (2006)

The voltage margin of a resistor-logic demultiplexer can be improved significantly by basing its connection pattern on a constant-weight code. Each distinct code determines a unique demultiplexer, and therefore a large family of circuits is defined. We consider using these demultiplexers for building nanoscale crossbar memories, and determine the voltage margin of the memory system based on a particular code. We determine a purely code-theoretic criterion for selecting codes that will yield memories with large voltage margins, which is to minimize the ratio of the maximum to the minimum Hamming distance between distinct codewords. For the specific example of a 64 × 64 crossbar, we discuss what codes provide optimal performance for a memory.
Novel mutations in UL24 and gH rescue efficient infection of an HSV vector retargeted to TrkA (2023)

Transductional targeting of herpes simplex virus (HSV)-based gene therapy vectors offers the potential for improved tissue-specific delivery and can be achieved by modification of the viral entry machinery to incorporate ligands that bind the desired cell surface proteins. The interaction of nerve growth factor (NGF) with tropomyosin receptor kinase A (TrkA) is essential for survival of sensory neurons during development and is involved in chronic pain signaling. We targeted HSV infection to TrkA-bearing cells by replacing the signal peptide and HVEM binding domain of glycoprotein D (gD) with pre-pro-NGF. This TrkA-targeted virus (KNGF) infected cells via both nectin-1 and TrkA. However, infection through TrkA was inefficient, prompting a genetic search for KNGF mutants showing enhanced infection following repeat passage on TrkA-expressing cells. These studies revealed unique point mutations in envelope glycoprotein gH and in U<sub>L</sub>24, a factor absent from mature particles. Together these mutations rescued efficient infection of TrkA-expressing cells, including neurons, and facilitated the production of a completely retargeted KNGF derivative. These studies provide insight into HSV vector improvements that will allow production of replication-defective TrkA-targeted HSV for delivery to the peripheral nervous system and may be applied to other retargeted vector studies in the central nervous system.
Lack of Association of BRCA1 and BRCA2 Variants with Breast Cancer in an Ethnic Population of Saudi Arabia, an Emerging High-Risk Area (2013)

Incidence of breast cancer shows geographical variation, even within areas of ethnic homogeneity. Saudi Arabia has witnessed an increase in occurrence of breast cancer in its unexplored ethnic populations over the past few years. We aimed at determining whether any association exists between single nucleotide polymorphisms in breast cancer associated gene 1 (BRCA1) and breast cancer associated gene 2 (BRCA2) and the risk of breast cancer. TaqMan based Real Time Polymerase chain reaction genotyping assays were used to determine the frequency of single nucleotide polymorphisms in BRCA1 (rs799917) and BRCA2 (rs144848) in a group of 100 breast cancer patients and unaffected age matched controls of Saudi Arabian origin. The present data revealed that neither BRCA1 nor the BRCA2 studied variant show any significant association with the disease. This study failed to find any role of the concerned variants in breast cancer either as risk or as prognostic factors. The small number of patients registered was one of the limitations of this study. In summary, comparison of mutation profile with other ethnic populations and regions reflected both differences and similarities indicating co-exposure to a unique set of risk factors. The differences could be due to exposure to particular environmental carcinogens; different lifestyle, reproductive pattern; dietary or cultural practices of Saudi Arabian women that need further investigations.
MATCHED FILTER-BOUND OF BANDWIDTH EFFICIENT MULTISCALE WAVELET SIGNALING OVER MULTIPATH RAYLEIGH FADING CHANNELS (1999)

International Telemetering Conference Proceedings / October 25-28, 1999 / Riviera Hotel and Convention Center, Las Vegas, Nevada
Treatment Parameters Optimization to Compensate for Interfractional Anatomy Variability and Intrafractional Tumor Motion (2015)

Scanned ion beam therapy of lung tumors is severely limited in its clinical applicability by intrafractional organ motion, interference effects between beam and tumor motion (interplay), as well as interfractional anatomic changes. To compensate for dose deterioration caused by intrafractional motion, motion mitigation techniques, such as gating, have been developed. However, optimization of the treatment parameters is needed to further improve target dose coverage and normal tissue sparing. The aim of this study was to determine treatment-planning parameters that permit to recover good target coverage for each fraction of lung tumor treatments. For 9 lung tumor patients from MD Anderson Cancer Center (Houston, Texas), a total of 70 weekly time-resolved computed tomography (4DCT) datasets, which depict the evolution of the patient anatomy over the several fractions of the treatment, were available. Using the GSI in-house treatment planning system TRiP4D, 4D simulations were performed on each weekly 4DCT for each patient using gating and optimization of a single treatment plan based on a planning CT acquired prior to treatment. The impact on target dose coverage (V 95%,CTV) of variations in focus size and length of the gating window, as well as different additional margins and the number of fields was analyzed. It appeared that interfractional variability could potentially have a larger impact on V 95%,CTV than intrafractional motion. However, among the investigated parameters, the use of a large beam spot size, a short gating window, additional margins, and multiple fields permitted to obtain an average V 95%,CTV of 96.5%. In the presented study, it was shown that optimized treatment parameters have an important impact on target dose coverage in the treatment of moving tumors. Indeed, intrafractional motion occurring during the treatment of lung tumors and interfractional variability were best mitigated using a large focus, a short gating window, additional margins, and three fields.
Role of the core-valence interaction for pseudopotential calculations with exact exchange (2001)

Standard normconserving pseudopotentials for the exact exchange energy functional of density functional theory exhibit a spurious long-range structure induced by the core-valence interaction. In this contribution the origin of this structure and its implications for the description of atoms, molecules, and solids is analyzed in detail. It is found that bond distances and energies obtained can be seriously in error, in particular for solids. Based on this analysis a parameter-free, self-consistent scheme for the elimination of the spurious feature is suggested. The resulting pseudopotentials predict binding properties of molecules and solids which, on average, are more accurate than those obtained with the corresponding local density approximation pseudopotentials.
Decentralized Global Transaction Management in Multidatabase Systems (1993)

This paper discusses the implementation of decentralized global transaction management in the multidatabase system environment without violation of local autonomy.The principal concern of this investigation has been to develop a method of global transaction management that is particularly suited to decentralized multidatabase systems.Global concurrency control and atomic commitment have been approached by allowing the serialization and commitment orders of global sub transactions to be determined at each local site, eliminating the need to transfer local information to the global level.Building upon these concepts, we propose a mechanism which supports a decentralized global transaction management approach, completely circumventing the difficulties posed by central coordination.As multidatabase systems integrate a large number of participating local database systems, a decentralized design is essential to the achievement of a high degree of fault-tolerance.
On the Use of ArXiv as a Dataset (2019)

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.
Lens Blocking Method for Opticam (1992)

A uv-curing 'cold' blocking adhesive has been developed by Loctite Corporation for use with the Opticam SM. The adhesive is a significant advance in the lens blocking process, as it eliminates heat-induced blocking strain; the most significant problem encountered with current hot pitch blocking methods. The new cold blocking adhesive is complemented by a new Kennametal lens blocking adapter tool and chucking system. The tooling offers substantially improved lens adapter to machine alignment and transfer, at considerably lower cost. The lenses are deblocked in a heated water and detergent solution, eliminating the environmental concerns of the current method.
Live ultrasound volume reconstruction using scout scanning (2015)

Use of scout scanning may allow the physician to identify anatomical structures. Subsequent live volume reconstruction in a region of interest may assist in procedures such as targeting needle interventions or estimating brain shift during surgery.
Oxalohydrazide Ligands for Copper‐Catalyzed C−O Coupling Reactions with High Turnover Numbers (2020)

Abstract Here, we report a class of ligands based on oxalohydrazide cores and N ‐amino pyrrole and N ‐amino indole units that generates long‐lived copper catalysts for couplings that form the C−O bonds in biaryl ethers. These Cu‐catalyzed coupling of phenols with aryl bromides occurred with turnovers up to 8000, a value which is nearly two orders of magnitude higher than those of prior couplings to form biaryl ethers and nearly an order of magnitude higher than those of any prior copper‐catalyzed coupling of aryl bromides and chlorides. This ligand also led to copper systems that catalyze the coupling of aryl chlorides with phenols and the coupling of aryl bromides and iodides with primary benzylic and aliphatic alcohols. A wide variety of functional groups including nitriles, halides, ethers, ketones, amines, esters, amides, vinylarenes, alcohols and boronic acid esters were tolerated, and reactions occurred with aryl bromides in pharmaceutically related structures.
Supplementary Data from Transcriptional Plasticity Drives Leukemia Immune Escape (2023)

Supplementary Data from Transcriptional Plasticity Drives Leukemia Immune Escape