gebhart/patrepeval huggingface dataset:
Switching in an Optical Interconnect Environment (1989)

Optical interconnects are gaining importance in a wide range of applications, ranging from interconnection of supercomputers and workstations to interconnection of multiple chips on a single board. With the development of any interconnect technology, eventually the need for switching arises. Thus the switching of optical interconnects is a topic of much current interest.
Fast Finite Width Neural Tangent Kernel (2022)

The Neural Tangent Kernel (NTK), defined as $Θ_θ^f(x_1, x_2) = \left[\partial f(θ, x_1)\big/\partial θ\right] \left[\partial f(θ, x_2)\big/\partial θ\right]^T$ where $\left[\partial f(θ, \cdot)\big/\partial θ\right]$ is a neural network (NN) Jacobian, has emerged as a central object of study in deep learning. In the infinite width limit, the NTK can sometimes be computed analytically and is useful for understanding training and generalization of NN architectures. At finite widths, the NTK is also used to better initialize NNs, compare the conditioning across models, perform architecture search, and do meta-learning. Unfortunately, the finite width NTK is notoriously expensive to compute, which severely limits its practical utility. We perform the first in-depth analysis of the compute and memory requirements for NTK computation in finite width networks. Leveraging the structure of neural networks, we further propose two novel algorithms that change the exponent of the compute and memory requirements of the finite width NTK, dramatically improving efficiency. Our algorithms can be applied in a black box fashion to any differentiable function, including those implementing neural networks. We open-source our implementations within the Neural Tangents package (arXiv:1912.02803) at https://github.com/google/neural-tangents.
High power factor control using load resonant frequency auto tracking phase shift inverter (2010)

This paper proposes a new method for frequency control and for output power control using a load resonant frequency auto tracking phase shift inverter. The proposed method employs a phase shift inverter with a single output current sensor. The fundamental waveform signal of the output voltage of a phase shift inverter is generated by using the proposed method because the conventional method produces an output voltage that has a pulse waveform. The proposed control strategy to utilize load resonant frequency easily achieves unity power factor control with high efficiency. In the proposed method, the fundamental waveform signal of the inverter output voltage coincides with the detected inverter output current wave form. Moreover, as the inverter output power is regulated by controlling the phase angle of each inverter leg using the proposed method, soft-switching control can be realized. The experimental results presented in this paper confirm the validity of the proposed methods.
Health seeking behavior after the 2013–16 Ebola epidemic: Lassa fever as a metric of persistent changes in Kenema District, Sierra Leone (2021)

Analysis of patient demographic data suggests that fewer individuals sought care for Lassa fever and other febrile illnesses in Kenema District after the West African Ebola epidemic. Re-establishing trust in health care services will require efforts beyond rebuilding infrastructure and require concerted efforts to rebuild the trust of local residents who may be wary of seeking healthcare post epidemic.
Synthesis of N-Heterocyclic Stannylene (Sn(II)) and Germylene (Ge(II)) and a Sn(II) Amidinate and Their Application as Precursors for Atomic Layer Deposition (2014)

Thin films containing germanium or tin have a great variety of current and potential applications, particularly their oxides or chalcogenides. Chemical vapor deposition (CVD) and atomic layer deposition (ALD) are popular ways to make these thin films conformally even on challenging nanostructured substrates. The success of these processes depends on having precursors that are sufficiently stable, volatile, and reactive. In this paper we optimize the syntheses of the following three precursors: 1 and 2 are racemic Ge(II) or Sn(II) cyclic amides made from N2,N3-di-tert-butylbutane-2,3-diamine, and 3 is bis(N,N′-diisopropylacetamidinato)tin(II). All three compounds are demonstrated to be effective precursors for ALD of their monosulfides, GeS or SnS, by reaction with H2S. 2 has also been reported previously to make polycrystalline SnO2 by ALD with oxidizing agents such as H2O2. The cyclic amides 1 and 2 are more volatile than the amidinate 3, vaporizing sufficiently for ALD even at precursor temperatures below 40 °C, whereas 3 vaporizes at temperatures over 90 °C. 1 and 2 can thus be used at lower substrate temperatures than 3. GeS or SnS can be deposited on substrates even at temperatures below 50 °C, while ALD of SnS from 3 becomes slow below substrate temperatures of 100 °C because of insufficient vapor pressure. The amount of growth per ALD cycle is higher for the cyclic amide 2 than for the amidinate 3. The GeS films are smooth and amorphous, while the SnS films are polycrystalline and granular. All of these films are uniformly thick inside holes with aspect ratios (depth/diameter) greater than 40:1.
Loss of diurnal behavioral rhythms and impaired lipid metabolism in growing pigs with mistimed feeding (2021)

The misalignment of eating time and the endogenous circadian rhythm impairs the body's ability to maintain homeostasis. Although it is well established that children and growing animals differ from adults in their energy metabolism and behavioral patterns, little is known about how mistimed feeding disturbs the diurnal rhythms of behavior and metabolism in children and growing diurnal animals. In this study, growing pigs (diurnal animal) were randomly assigned to the daytime-restricted feeding (DRF) and nighttime-restricted feeding (NRF) groups for 5 weeks. Compared with observations in the DRF group, NRF disrupted the diurnal rhythm of behavior and clock genes and lowered the serum ghrelin, dopamine, and serotonin levels during the daytime and nighttime. Microbiome analysis results suggested that NRF altered the diurnal rhythm and composition of the gut microbiota, and increased log-ratios of Catenibacterium:Butyrivibrio and Streptococcus:Butyrivibrio. Based on the serum proteome, the results further revealed that rhythmic and upregulated proteins in NRF were mainly involved in oxidative stress, lipid metabolism, immunity, and cancer biological pathways. Serum physiological indicators further confirmed that NRF decreased the concentration of melatonin and fibroblast growth factor 21 during the daytime and nighttime, increased the diurnal amplitude and concentrations of very-low-density lipoprotein cholesterol, triglyceride, and total cholesterol, and increased the apolipoprotein B/ApoA1 ratio, which is a marker of metabolic syndrome. Taken together, this study is the first to reveal that mistimed feeding disrupts the behavioral rhythms of growing pigs, reprograms gut microbiota composition, reduces the serum levels of hormones associated with fighting depression and anxiety, and increases the risk of lipid metabolic dysregulation.
Effect of a Novel Antibiotic, Heliquinomycin, on DNA Helicase and Cell Growth. (1998)

Heliquinomycin, a novel microbial product, was found to inhibit a human DNA helicase enzyme isolated from HeLa S3 cells at concentrations of 5 to 10 micrograms/ml. In contrast, adriamycin, etoposide and cisplatin did not inhibit this enzyme at the concentrations tested. Furthermore, the replication and repair of SV40 chromosome were not affected at heliquinomycin concentration of 50 micrograms/ml. The topoisomerase II and I enzymes were inhibited at 30 micrograms/ml and 100 micrograms/ml of heliquinomycin, respectively. Heliquinomycin inhibited the growth of HeLa S3, KB, LS180, K562 and HL60 human tumor cell lines at IC50 values of 0.96 to 2.8 micrograms/ml. In addition, the growth of adriamycin and cisplatin resistant P388 cell lines were inhibited at similar concentrations. Heliquinomycin inhibited both DNA and RNA synthesis in cell culture but did not inhibit protein synthesis. HeLa S3 cells were arrested at the G2/M phase by heliquinomycin. These studies suggest that heliquinomycin is a selective inhibitor of a cellular DNA helicase and in turn, inhibits growth of tumor cell lines.
Sound content analysis for indexing and understanding (2000)

Discusses speech recognition, auditory scene analysis, and content-based indexing and retrieval.
Mobile poultry processing units: a safe and cost-effective poultry processing option for the small-scale farmer in the United States (2014)

AbstractIn developed countries, small farmer entrepreneurs contemplating poultry production are becoming more interested in assessing mobile poultry processing units (MPPU) to add additional value to the birds they sell in urban or farmers' markets. However, there continues to be a lack of viable poultry processing options for small flocks as evidenced by the recent United States Department of Agriculture map, which depicts the locations of both small farms and processing facilities, county by county, across the United States. This map substantiates the need for more affordable poultry processing options to serve small-scale farmers. Many small-scale farmers operate MPPUs under federal exemptions that exclude them from continuous inspections by the USDA's Food Safety and Inspection Service, but they are still required to meet all sanitation and wholesomeness requirements. Costs associated with processing are somewhat less under this exemption, but one is unable to sell poultry as having been inspected in the open market. The USDA-FSIS has also created a mobile slaughter unit compliance guide for those who wish to be USDA regulated. Either way, regulated or unregulated, the MPPU may be an affordable and efficient solution to add value to small flock production. Small-scale poultry farmers, both organic and pastured, may benefit from the opportunities associated with mobile processing.Keywords:: mobile poultry processingsmall-scale farmertraining AcknowledgementsThis review was funded by SARE grant LS11-245 to authors Alali, Kostadini, Gibson, Ricke, Jaroni, and Crandall.
Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions (2023)

Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-<i>manno</i>-oct-2-ulosonic acid (Kdo)<sub>2</sub>-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
Battery Power Efficiency of PPM and FSK in Wireless Sensor Networks (2007)

As sensor nodes are typically powered by nonrenewable batteries, energy efficiency is a critical factor in wireless sensor networks (WSNs). Orthogonal modulations appropriate for the energy-limited WSN setup have been investigated under the assumption that batteries are linear and ideal, but their effectiveness is not guaranteed when more realistic nonlinear battery models are considered. In this paper, based on a general model that integrates typical WSN transmission and reception modules with realistic battery models, we derive two battery power-conserving schemes for two M-ary orthogonal modulations, namely pulse position modulation (PPM) and frequency shift keying (FSK), both tailored for WSNs. Then we analyze and compare the battery power efficiency of PPM and FSK over various wireless channel models. Our results reveal that FSK is more power-efficient than PPM in sparse WSNs, while PPM may outperform FSK in dense WSNs. We also show that in sparse WSNs, the power advantage of FSK over PPM is no more than 3 dB; whereas in very dense WSNs, the power advantage of PPM over FSK can be much more significant as the constellation size M increases.
Effect of Sequence Polymorphisms on Performance of Two Real-Time PCR Assays for Detection of Herpes Simplex Virus (2005)

Herpes simplex virus (HSV) is the most common cause of acquired, sporadic encephalitis in the United States. PCR identification of HSV in spinal fluid has become the diagnostic gold standard due to its sensitivity and potential for speed, replacing other methods such as culture. We developed a real-time PCR assay to detect HSV, using a new type of hybridization probe, the Eclipse probe. In this study, we ran 323 samples (171 positives and 152 negatives) with the Eclipse real-time PCR assay and compared these results with another PCR assay using gel detection. The real-time assay agreed with our reference method for 319 out of the 323 samples tested (99%). Using two different real-time PCR platforms, we discovered that SNPs within the amplicon's probe binding region that are used to distinguish HSV-1 from HSV-2 can decrease assay sensitivity. This problem is potentially a general one for assays using fluorescent probes to detect target amplification in a real-time format. While real-time PCR can be a powerful tool in the field of infectious disease, careful sequence evaluation and clinical validation are essential in creating an effective assay.
Ipsilesional neglect: Behavioral and anatomical correlates. (2014)

Our data confirm previous research suggesting that ipsilesional neglect may result from lesions to the right frontal-subcortical networks. Furthermore, in our group, ipsilesional neglect was also strongly associated with primarily "where" perceptual-attentional bias, and less so with "aiming" motor-intentional spatial bias.
Sports Concussion And Mild Traumatic Brain Injury Assessment Is Enhanced With Portable, Non-invasive Biosensor Arrays (2015)

PURPOSE: To determine the degree that sports concussion may be identified by predictive multivariate models including neuropsychological testing data, single-lead electroenceplographic (EEG) data, and other modes of biosensor data. METHODS: Collegiate athletes who suffered traumatic brain injury (concussion; N=30) while participating in varsity sports were assessed in a longitudinal study design during the symptomatic and asymptomatic phase of recovery. These data were compared to an equal number of non-injured, age matched, comparator subjects. Each participant was tested using a novel single-lead EEG device during a series of cognitive and behavioral tasks, including eyes closed (EC) and eyes open (EO) resting task and a five word immediate recall task under IRB supervision. Behavioral measures (e.g. error-rate/task duration) and EEG spectral and wavelet features were extracted from EC/EO baseline and neuropsychological test epochs. Univariate and multivariate logistic regression, linear discriminant analysis and random forest models were compared for the ability to predict a concussive event as well as to develop signatures of Return-to-Learn and Return-to-Play decisions. RESULTS: EEG spectral density power features (e.g. relative beta power), relative to overall power, had an overall predictive accuracy of 65% (p<0.004). Additionally, total read times alone were 62% accurate (p<0.015) in a neuro-ophthalmologic saccade test. In a multivariate model, these two modes were found to be 70% accurate (p<0.006). However, inclusion of covariates increased discriminant power to 76% accurate at differentiating concussed from control subjects (p<0.003). CONCLUSIONS: Neuropsychological testing benefits by the addition of other objective biosensor modalities in the predictive performance of concussion / TBI testing for both the identification and management in Return-to-Learn and Return-to-Play decision making. These results suggest the use of multivariate signatures for concussion/TBI testing. Nonetheless, these preliminary findings must be independently replicated, validated, and expanded in sample size across multiple clinical settings such as team sports and emergency department use.
Cashew Nut Shells Pyrolysis:  Individual Gas Evolution Rates and Yields (2007)

Cashew nut shells are one type of the most abundant biomass tropical wastes, which can be used for energy generation. However, there is lack of data for the thermal conversion process of cashew nut shells such as pyrolysis individual gas products, yields, and reaction kinetics. In this research work, the pyrolysis processes of cashew nut shells at low heating rates (10, 30, and 100 K/min) were studied. Thermogravimetric analyzer coupled with a Fourier transform infrared spectrometer (TG-FTIR) was used. The pyrolysis product yields obtained were compared with the available data in the literature for wood and Miscanthus Giganteus. It was found that cashew nut shells have tars and volatiles at levels equivalent to those of wood pellets, both above the tar and volatile content of M. Giganteus. Further, kinetic parameters were obtained from the TG-FTIR results using an approach based on parallel independent first-order reactions with a Gaussian distribution of activation energies and following the Tmax method. The data obtained through this approach included the identification, kinetics, and yield of each gas product precursor. These results are then used as input files for a distributed activation energy model (DAEM) for biomass pyrolysis, based on a functional group analysis, which still does not include the devolatilization, cross-linking competitive reactions. The predicted evaluation data from this model were found to generally agree with that from TG-FTIR analysis. However, the model still demands improvement to accommodate secondary and cross-linking competitive reactions.
Refresh pausing in DRAM memory systems (2014)

Dynamic Random Access Memory (DRAM) cells rely on periodic refresh operations to maintain data integrity. As the capacity of DRAM memories has increased, so has the amount of time consumed in doing refresh. Refresh operations contend with read operations, which increases read latency and reduces system performance. We show that eliminating latency penalty due to refresh can improve average performance by 7.2%. However, simply doing intelligent scheduling of refresh operations is ineffective at obtaining significant performance improvement. This article provides an alternative and scalable option to reduce the latency penalty due to refresh. It exploits the property that each refresh operation in a typical DRAM device internally refreshes multiple DRAM rows in JEDEC-based distributed refresh mode. Therefore, a refresh operation has well-defined points at which it can potentially be Paused to service a pending read request. Leveraging this property, we propose Refresh Pausing , a solution that is highly effective at alleviating the contention from refresh operations. It provides an average performance improvement of 5.1% for 8Gb devices and becomes even more effective for future high-density technologies. We also show that Refresh Pausing significantly outperforms the recently proposed Elastic Refresh scheme.
Transcriptomic response of brain tissue to focused ultrasound‐mediated blood–brain barrier disruption depends strongly on anesthesia (2020)

Focused ultrasound (FUS) mediated blood-brain barrier disruption (BBBD) targets the delivery of systemically-administered therapeutics to the central nervous system. Preclinical investigations of BBBD have been performed on different anesthetic backgrounds; however, the influence of the choice of anesthetic on the molecular response to BBBD is unknown, despite its potential to critically affect interpretation of experimental therapeutic outcomes. Here, using bulk RNA sequencing, we comprehensively examined the transcriptomic response of both normal brain tissue and brain tissue exposed to FUS-induced BBBD in mice anesthetized with either isoflurane with medical air (Iso) or ketamine/dexmedetomidine (KD). In normal murine brain tissue, Iso alone elicited minimal differential gene expression (DGE) and repressed pathways associated with neuronal signaling. KD alone, however, led to massive DGE and enrichment of pathways associated with protein synthesis. In brain tissue exposed to BBBD (1 MHz, 0.5 Hz pulse repetition frequency, 0.4 MPa peak-negative pressure), we systematically evaluated the relative effects of anesthesia, microbubbles, and FUS on the transcriptome. Of particular interest, we observed that gene sets associated with sterile inflammatory responses and cell-cell junctional activity were induced by BBBD, regardless of the choice of anesthesia. Meanwhile, gene sets associated with metabolism, platelet activity, tissue repair, and signaling pathways, were differentially affected by BBBD, with a strong dependence on the anesthetic. We conclude that the underlying transcriptomic response to FUS-mediated BBBD may be powerfully influenced by anesthesia. These findings raise considerations for the translation of FUS-BBBD delivery approaches that impact, in particular, metabolism, tissue repair, and intracellular signaling.
Chronic treatment with exendin(9–39)amide indicates a minor role for endogenous glucagon-like peptide-1 in metabolic abnormalities of obesity-related diabetes in ob/ob mice (2005)

Glucagon-like peptide-1 (GLP-1) is a potent insulinotropic hormone proposed to play a role in both the pathophysiology and treatment of type 2 diabetes. This study has employed the GLP-1 receptor antagonist, exendin-4(9-39)amide (Ex(9-39)) to evaluate the role of endogenous GLP-1 in genetic obesity-related diabetes and related metabolic abnormalities using ob/ob and normal mice. Acute in vivo antagonistic potency of Ex(9-39) was confirmed in ob/ob mice by blockade of the insulin-releasing and anti-hyperglycaemic actions of intraperitoneal GLP-1. In longer term studies, ob/ob mice were given once daily injections of Ex(9-39) or vehicle for 11 days. Feeding activity, body weight, and both basal and glucose-stimulated insulin secretion were not significantly affected by chronic Ex(9-39) treatment. However, significantly elevated basal glucose concentrations and impaired glucose tolerance were evident at 11 days. These disturbances in glucose homeostasis were independent of changes of insulin sensitivity and reversed by discontinuation of the Ex(9-39) for 9 days. Similar treatment of normal mice did not affect any of the parameters measured. These findings illustrate the physiological extrapancreatic glucose-lowering actions of GLP-1 in ob/ob mice and suggest that the endogenous hormone plays a minor role in the metabolic abnormalities associated with obesity-related diabetes.