gebhart/patrepeval huggingface dataset:
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction (2000)

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs called and, respectively. performed well at exact identification of coding exons in 117 orthologous pairs tested.
Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. (2020)

Recent research in predicting protein secondary structure populations (SSP) based on Nuclear Magnetic Resonance (NMR) chemical shifts has helped quantitatively characterise the structural conformational properties of intrinsically disordered proteins and regions (IDP/IDR). Different from protein secondary structure (SS) prediction, the SSP prediction assumes a dynamic assignment of secondary structures that seem correlate with disordered states. In this study, we designed a single-task deep learning framework to predict IDP/IDR and SSP respectively; and multitask deep learning frameworks to allow quantitative predictions of IDP/IDR evidenced by the simultaneously predicted SSP. According to independent test results, single-task deep learning models improve the prediction performance of shallow models for SSP and IDP/IDR. Also, the prediction performance was further improved for IDP/IDR prediction when SSP prediction was simultaneously predicted in multitask models. With p53 as a use case, we demonstrate how predicted SSP is used to explain the IDP/IDR predictions for each functional region.
First‐in‐Human Study of Bamlanivimab in a Randomized Trial of Hospitalized Patients With COVID‐19 (2021)

Therapeutics for patients hospitalized with coronavirus disease 2019 (COVID-19) are urgently needed during the pandemic. Bamlanivimab is a potent neutralizing monoclonal antibody that blocks severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) attachment and entry into human cells, which could potentially lead to therapeutic benefit. J2W-MC-PYAA was a randomized, double-blind, sponsor unblinded, placebo-controlled, single ascending dose first-in-human trial (NCT04411628) in hospitalized patients with COVID-19. A total of 24 patients received either placebo or a single dose of bamlanivimab (700 mg, 2,800 mg, or 7,000 mg). The primary objective was assessment of safety and tolerability, including adverse events and serious adverse events, with secondary objectives of pharmacokinetic (PK) and pharmacodynamic analyses. Treatment-emergent adverse event (TEAE) rates were identical in the placebo and pooled bamlanivimab groups (66.7%). There were no apparent dose-related increases in the number or severity of TEAEs. There were no serious adverse events or deaths during the study, and no discontinuations due to adverse events. PKs of bamlanivimab is linear and exposure increased proportionally with dose following single i.v. administration. The half-life was ~ 17 days. These results demonstrate the favorable safety profile of bamlanivimab, and provided the initial critical evaluation of safety, tolerability, and PKs in support of the development of bamlanivimab in several ongoing clinical trials.
Supplementary Figure 5 from Mature Cytotoxic CD56<sup>bright</sup>/CD16<i><sup>+</sup></i> Natural Killer Cells Can Infiltrate Lymph Nodes Adjacent to Metastatic Melanoma (2023)

&lt;p&gt;PDF file - 450K, Phenotype of blood NK cells from stage III melanoma patients.&lt;/p&gt;
Investigation of light-emission and avalanche-current mechanisms in PureB SPAD devices (2019)

The light emission from silicon PureB photodiodes was investigated in both forward- and avalanchemode operation and correlated to the presence of process-dependent defects that influence the reverse IV characteristics. As opposed to “defect-free” diodes with low dark currents and abrupt breakdown behavior, the diodes with defects had higher current levels and light-emitting spots appearing at voltages far below the breakdown voltage otherwise set by the implemented doping profiles. The role of such defect-related behavior for the application of the photodiodes as single-photon avalanche diodes (SPADs) and avalanche-mode light-emitting diodes (AMLEDs) is assessed in connection with the recent demonstration of these basic devices as both the light-emitting and light-detecting elements in optocoupler circuits integrated in CMOS for data transmission purposes.
MicroRNA-551b expression profile in low and high-grade cervical intraepithelial neoplasia. (2018)

Our data showed a significant inverse correlation between miR-551b expression and the histological grading of the lesions, suggesting a tumor suppressive function in the different stages of cervical dysplasia.
EXPLORATION OF THE ROLE OF B7H4 IN CHRONIC ALLOGRAFT VASCULOPATHY (2008)

Transplantation: July 27, 2008 - Volume 86 - Issue 2S - p 510-511 doi: 10.1097/01.tp.0000331149.56389.99
Prognosefaktoren der offenen Abdominalbehandlung in der Viszeralchirurgie (2017)

<b>Introduction</b> In general surgery, open abdomen treatment (OAT) is used to treat abdominal compartment syndrome (ACS) and sepsis, often after a primary surgical procedure associated with complications. The results achieved in this patient population may depend on factors that are yet unknown. This study evaluates independent patient-related prognostic factors after OAT. <b>Methods</b> 38 clinical parameters and survival data of 165 consecutive general surgery patients after OAT were entered into a prospective database according to a defined algorithm in order to analyse the underlying surgical pathology, predictors of survival and important aspects of OAT-related morbidity. Independent predictors of survival, OAT-related morbidity and duration of hospital stay were identified. <b>Results</b> Common indications for OAT were peritonitis, haemorrhage and ACS. Median age was 60 years and > 80 % of patients were ASA III/IV; median follow-up was 23 months. Oncologic surgery was performed in 19 % of cases. 30-day and 1-year mortality was 11 % and 34 %, respectively. Malignancy was a negative predictor (OR: 4.63, 95 % CI: 2.00-10.7) while mild obesity (BMI 25-35) and primary fascial closure, which was achieved in 82 % of patients, improved survival (OR: 0.2, 95 % CI: 0.07-0.55; OR: 0.19, 95 % CI: 0.06-0.57). Enteroatmospheric fistula (EAF) and giant hernia with impossible fascial closure were frequent after OAT (19 and 18 %), and malignancy was an independent risk factor for EAF (OR 3.47, CI [95 %]: 1.41-8.53). Vacuum-assisted wound closure or polyglactin mesh interposition did not affect EAF incidence. <b>Conclusions</b> General surgery patients after OAT differ significantly from trauma patients, and mortality as well as long-term morbidity is high. Outcome is greatly determined by independent patient-related factors after OAT. A tailored surgical approach based on objective evidence is needed to further improve the results after OAT.
Measurement of the ratio of the inclusive 3-jet cross section to the inclusive 2-jet cross section in pp collisions at $\sqrt{s} = 7\ \mathrm{TeV}$ and first determination of the strong coupling constant in the TeV range (2013)

A measurement is presented of the ratio of the inclusive 3-jet cross section to the inclusive 2-jet cross section as a function of the average transverse momentum, pT1,2 , of the two leading jets in the event. The data sample was collected during 2011 at a proton-proton centre-of-mass energy of 7 TeV with the CMS detector at the LHC, corresponding to an integrated luminosity of 5.0 fb-1. The strong coupling constant at the scale of the Z boson mass is determined to be S (M Z)=0.11480.0014 (exp.)0.0018 (PDF)0.0050(theory), by comparing the ratio in the range 0.42<pT1,2<1.39 TeV to the predictions of perturbative QCD at next-to-leading order. This is the first determination of S (M Z) from measurements at momentum scales beyond 0.6 TeV. The predicted ratio depends only indirectly on the evolution of the parton distribution functions of the proton such that this measurement also serves as a test of the evolution of the strong coupling constant. No deviation from the expected behaviour is observed.
Optical characterization of multi-NST nanowire test structures using Mueller matrix spectroscopic ellipsometry (MMSE) based scatterometry for sub 5nm nodes (2019)

With the rapid advancement of the CMOS technology in the semiconductor industry, innovative device fabrication techniques have led to the development of Nanosheet (NS) FETs and Nanowire (NW) FETs with sub nm dimensions. The application of Mueller Matrix Spectroscopic Ellipsometry (MMSE) based scatterometry simulations to characterize these complex 3D structures is described. Optical model-based simulations were used to investigate sensitivity and limitations of MMSE to characterize small changes in the etching of these NWTS structures. Cross-sectional Scanning Electron Microscopy and Tunneling Electron Microscopy provided a reference technique for the scatterometry simulations. Additionally, sensitivity to the nanowire test structure shape, size of holes, nanosheet thicknesses of each layer and the rounding at the top of the structure were investigated. As a result of this study, we find that Mueller Matrix scatterometry has the sensitivity to monitor dimensional changes during the progression of the selective SiGe etch for the sub surface nanowires and thus provide a reliable measurement method for process control.
Proceedings of the NIPS'93 Postconference Workshop on Pulling It All Together: Methods for Combining Neural Networks (1994)

Abstract : This report is the proceedings from the NIPS'93 postconference workshop entitled 'Pulling It All Together: Methods for Combining Neural Networks.' The goal of the workshop was to examine theoretical aspects and heuristic methods for combining existing neural network algorithms to generate systems which have improved performance properties. This report includes an outline and summary of the workshop as well as the slides used in each participant's presentation. Averaging, Ensemble methods, Committees.
Supplementary Figure Legends from Combination Immunotherapy after ASCT for Multiple Myeloma Using MAGE-A3/Poly-ICLC Immunizations Followed by Adoptive Transfer of Vaccine-Primed and Costimulated Autologous T Cells (2023)

&lt;p&gt;PDF file - 48KB&lt;/p&gt;
Fault-based test methodology for analog amplifier circuits (2017)

This paper presents a technique for the fault-based test of the analog amplifiers. The circuit defects are modeled with the 2-fault transistor models. The test method combines the amplifier evaluation both in and out of the normal operating region, with the transconductance of the amplifier being the key test parameter. Furthermore, the additional low current test is employed in order to maximize the fault coverage. With all tests performed only at DC, the test time is significantly reduced. The test method is applicable to amplifiers with various structures. The fault-based simulation performed on a typical two-stage operational transconductance amplifier (OTA) exhibits 100% fault coverage.
Figure S2 from Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction (2023)

&lt;p&gt;Exposure to death receptor impaired tumor cells results in progressive CART19 dysfunction.&lt;/p&gt;
Direct Multi-Lateral Wafer Bonding for New Functionality in Photonic Integrated Circuits (2006)

This paper demonstrates direct wafer bonding along multiple cleaved facets in a single bonding step. This enables monolithic photonic integrated circuits with new functionality that cannot be realized by traditional integration approaches such as re-growth or selective area growth. We demonstrate the utility of this new technique in fabricating monolithic coarse wavelength division multiplexed (CWDM) laser arrays and ultra-broadband superluminescent diodes.
Effect of fenestrated stents on the renal arteries: Investigation of hemodynamic changes in abdominal aortic aneurysms treated with fenestrated endovascular grafts (2008)

This article uses a novel method of combining 3D image visualization and computational fluid dynamics to investigate the potential effect of fenestrated stents on the renal arteries in terms of blood flow pattern, flow rate at different cardiac cycles, based on patients with abdominal aortic aneurysm treated with fenestrated stent grafts. 3D imaging appearance of the fenestrated stents inserted into the renal arteries is used to guide the simulation of the stent protrusion into the abdominal aorta model for analysis of hemodynamic changes. A circular stent protrusion with a length of between 5-7 mm inside the abdominal aorta is simulated in two aorta models, and computational fluid dynamics is performed to detect the change of flow pattern and flow rate at the renal arteries. Our results demonstrate change of the renal flow rate is minimal following implantation of fenestrated stents, indicating the safety of fenestrated stent graft repair of patients with aortic aneurysms.
Home-use Photobiomodulation Device Treatment Outcomes for COVID-19 (2022)

ABSTRACT BACKGROUND There is need for non-pharmaceutical treatments for COVID-19. A home-use photobiomodulation (PBM) device was tested as Treatment in a randomized clinical trial. METHODS 294 patients were randomized with equal allocation to Treatment or Standard of Care (Control). 199 qualified for efficacy analyses. The Treatment group self-treated for 20 minutes twice daily, for the first 5 days, and subsequently once daily for 30 days. A validated respiratory questionnaire was used, and patients were monitored remotely. The primary endpoint was the time-to-recovery (3 consecutive days of no sickness) for general sickness. The Kaplan-Meier method and the Cox Proportional Hazards model were primary methods of analyses. RESULTS Treatment patients with collective 0-12 days of symptoms, at moderate-to-severe level on Day 1 of Treatment, did not recover significantly faster than Control. However, for patients with 0-7 days of symptoms there was a significant mean difference of 3 days: Treatment, 18 days (95% CI, 13-20) vs. Control, 21 days (95% CI, 15-28), P=0.050. The Treatment:Control hazard ratio at 1.495 (95% CI, 0.996-2.243), P=0.054 exceeded the pre-trial target of 1.44. Treated patients exceeding 7 days symptoms duration were more tired and had lower energy. None of the patients in the Treatment group suffered death or hospitalization while the Control group had 1 death and 3 severe adverse events requiring hospitalization. CONCLUSIONS Patients with up to 7 days of symptoms at moderate-to-severe levels on first day of Treatment can expect faster recovery for general sickness and several respiratory symptoms. (Funded by Vielight Inc.; ClinicalTrials.gov number, NCT04418505 .)
Design and Analysis of a Three-Phase Wireless Charging System for Lightweight Autonomous Underwater Vehicles (2017)

Lightweight autonomous underwater vehicles (AUVs), powered by rechargeable batteries, are widely deployed in inshore surveying, environmental monitoring, and mine countermeasures. While providing valuable information in locations humans have difficulty accessing, limited battery capacity of such systems prevents extended mission times. In order to extend mission times, this paper proposes a three-phase wireless charging system that could be used in a field-deployable charging station capable of rapid, efficient, and convenient AUV recharging. Wireless charging should not, however, affect instrumentation located inside the AUV. Thus, a three-dimensional finite element analysis tool is employed to study the characteristics of magnetic fields inside the AUV during three-phase charging. Simulation results reveal that the magnetic field generated by the proposed three-phase coil structure is concentrated away from the center of the AUV, where instrumentation would nominally be located. Detailed circuit analysis and compensation method to achieve resonance on both transmitter's and receiver's sides are also given. To validate the proposed concept, a three-phase wireless charging system is developed. Experimental results demonstrate that the system is able to transfer 1.0 kW with a dc-dc efficiency of 92.41% at 465 kHz.
Aging performances and cycle-life predictions of Li-ion battery (2016)

The state of health and cycle life predictions of power battery are the key points to battery monitoring and maintenance. For the purpose of solving this problem, firstly this paper set up battery experimental platform and collects battery change/discharge data. Then aging performances are analyzed according to the data and battery remaining useful life is predicted using data-driven methods. Finally, -the results of BP algorithm and SVM algorithm being used in the predictions are evaluated. The results indicate that the SVM algorithm is more efficient in the cycle life predictions of Li-ion cells.
Synapse formation and morphological differentiation of neuron types in embryonic rat dentate gyrus explants in vitro (1998)

Cultured explants obtained from the dentate gyrus of rat embryos (embryonic day 19-20) were used to investigate synapse formation and morphological differentiation of neuron types in the absence of extrinsic afferents. Synaptogenesis was studied by whole-cell recordings of postsynaptic currents and by ultrastructural analysis. Neurons were visualized using Lucifer Yellow filling or staining with DiI. In short-term (3-5 days) cultured explants postsynaptic currents were rarely evoked by extracellular stimulation and synapses were almost completely absent at the ultrastructural level. After 6-10 days in vitro, the incidence of evoking postsynaptic currents mediated by glutamate and GABA(A) receptors was strongly increased. At the ultrastructural level, the density of synapses increased more than 20-fold. These results demonstrate de novo formation of synapses in cultured embryonic dentate gyrus explants. Neuron types could be discriminated by their dendritic arborizations and by their electrophysiological properties. After 6-10 days in vitro, mossy-like cells exhibited 3-4 primary dendrites branching in a characteristic pattern and showed moderate spike-frequency adaptation. Application of serotonin (5-HT) to cultured explants elicited GABA(A)-receptor-mediated postsynaptic currents in mossy-like cells, indicating synaptic GABA release from local interneurons. Comparison to 5-HT evoked GABA release in mossy cells in age-matched, acute slices revealed only slight quantitative differences. In contrast to mossy cells, granule cells showing several primary dendrites originating at one cell pole were almost completely absent in cultured explants, suggesting an involvement of extrinsic afferents in the differentiation of granule cells.
Evaluating classifiers by means of test data with noisy labels (2003)

Often the most expensive and time-consuming task in building a pattern recognition system is collecting and accurately labeling training and testing data. In this paper, we explore the use of inexpensive noisy testing data for evaluating a classifier&amp;apos;s performance. We assume 1) the (human) labeler provides category labels with a known mislabeling rate and 2) the trained classifier and the labeler are statistically independent. We then derive the number of &amp;amp;quot;noisy &amp;amp;quot; test samples that arc, on average, equivalent to a single perfectly labeled test sample for the task of evaluating the classifier&amp;apos;s performance. For practical and realistic error and mislabeling rates, this number of equivalent test patterns can be surprisingly low. We also derive an upper and lower bound for the true error rate when the labeler and the classifier are not independent. 1
Family Attitudes regarding Newborn Screening for Krabbe Disease: Results from a Survey of Leukodystrophy Registries (2020)

Newborn screening (NBS) for Krabbe disease (KD) is currently underway in eight states in the USA, and there is continued discussion of whether to implement KD NBS in additional states. Workgroup members sought to survey a large number of families affected by KD. Families in KD and leukodystrophy family registries were contacted to seek their participation in <i>The Krabbe Newborn Screening-Family Perspective Survey</i>. The 170 respondents are comprised of the following: 138 family members with a KD individual diagnosed after development of symptoms, 20 notified about KD via NBS, and 12 with a KD individual diagnosed through family history of KD. The key results are that all NBS families with an early-infantile KD family member elected to pursue hematopoietic stem cell transplantation therapy. Of the 170 responders, 165 supported the implementation of KD NBS in all states in the USA.
High Risk Population Isolate Reveals Low Frequency Variants Predisposing to Intracranial Aneurysms (2014)

3% of the population develops saccular intracranial aneurysms (sIAs), a complex trait, with a sporadic and a familial form. Subarachnoid hemorrhage from sIA (sIA-SAH) is a devastating form of stroke. Certain rare genetic variants are enriched in the Finns, a population isolate with a small founder population and bottleneck events. As the sIA-SAH incidence in Finland is >2× increased, such variants may associate with sIA in the Finnish population. We tested 9.4 million variants for association in 760 Finnish sIA patients (enriched for familial sIA), and in 2,513 matched controls with case-control status and with the number of sIAs. The most promising loci (p<5E-6) were replicated in 858 Finnish sIA patients and 4,048 controls. The frequencies and effect sizes of the replicated variants were compared to a continental European population using 717 Dutch cases and 3,004 controls. We discovered four new high-risk loci with low frequency lead variants. Three were associated with the case-control status: 2q23.3 (MAF 2.1%, OR 1.89, p 1.42×10-9); 5q31.3 (MAF 2.7%, OR 1.66, p 3.17×10-8); 6q24.2 (MAF 2.6%, OR 1.87, p 1.87×10-11) and one with the number of sIAs: 7p22.1 (MAF 3.3%, RR 1.59, p 6.08×-9). Two of the associations (5q31.3, 6q24.2) replicated in the Dutch sample. The 7p22.1 locus was strongly differentiated; the lead variant was more frequent in Finland (4.6%) than in the Netherlands (0.3%). Additionally, we replicated a previously inconclusive locus on 2q33.1 in all samples tested (OR 1.27, p 1.87×10-12). The five loci explain 2.1% of the sIA heritability in Finland, and may relate to, but not explain, the increased incidence of sIA-SAH in Finland. This study illustrates the utility of population isolates, familial enrichment, dense genotype imputation and alternate phenotyping in search for variants associated with complex diseases.