gebhart/patrepeval huggingface dataset:
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences (2021)

These results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.
Influence of Smoking and Alcohol during Pregnancy on Outcome of VLBW Infants (2013)

Smoking during pregnancy results in a high rate of growth restricted VLBW infants. Prenatal exposition to nicotine seems to increase postnatal complications such as BPD und ROP.
Automation of analysis of cardiovascular autonomic function from chronic measurements of arterial pressure in conscious rats (2005)

At present, there is no single software package that provides a comprehensive power spectral analysis of pulse interval (PI) and arterial blood pressure (BP), spontaneous cardiac baroreceptor reflex gain (sBRG) and respiratory rate. Furthermore, scientific validation of the software that is currently commercially available and employed has not been published. We introduce 'Hey-Presto' software, which fully evaluates cardiovascular autonomic function from the BP signal obtained from rats. The program performs power spectral analysis of HR and BP variability, respiratory rate and, based on a time-series method, spontaneous cardiac baroreceptor (sBRG). We have validated Hey-Presto with conventional pharmacological agents to block cardiac vagal and cardiac sympathetic transmission in conscious rats fitted with a radio-telemetery BP transducer. Following administration of atropine (1 mg kg(-1), I.V.), high-frequency (HF) power of the PI decreased (P < 0.01) and was associated with the expected increase in HR. Subsequent cardiac sympathetic blockade (atenolol, 1 mg kg(-1), I.V.) reduced the low frequency (LF) to HF ratio (LF:HF) of the PI (P < 0.01), which was consistent with the observed reduction in HR. We also found that alterations in sBRG after blockade of cardiac autonomic transmission were highly comparable to values computed manually using vasoactive drugs administered intravenously. The software also detected circadian rhythms in sBRG, HF component of the PI, LF:HF of the PI and LF component of the BP as well as BP and HR during continuous 24 h recording. By demonstrating its application to humans, we found appropriate changes in the power of PI and the LF power of the BP during postural changes. These results demonstrate that Hey-Presto allows a fully automated, reliable, fast and comprehensive evaluation of cardiovascular autonomic function based on chronic measurements of BP in rats. Moreover, we have confirmed its versatility by demonstrating its application to man.
V 2 O 5 nanowire-based nanoelectronic devices for helium detection (2005)

The electrical responses of vanadium pentoxide nanowires to helium gas and environmental pressures are demonstrated. The devices feature well-aligned nanowires that are oriented by electrophoresis technique in the submicron scale. The electrical conductance is found to increase and decrease upon exposure to helium gas and air, respectively. This electrical response to helium is due to physical adsorption of the helium atoms into the interlayer of vanadium pentoxide nanowires. Furthermore, we observe flow-rate-dependent conductance variations such that the conductance is increased with stepwise behavior to the increase of flow rate of helium.
Assessing the safety and pharmacokinetics of the monoclonal antibodies, VRC07-523LS and PGT121 in HIV negative women in South Africa: study protocol for the CAPRISA 012A randomised controlled phase I trial (2019)

PACTR201808919297244; Pre-results.
A Facile, Convenient and Selective Homolytic Carbamolylation of Heteroaromatic Bases (1993)

The oxidative decarboxylation of monoamides of oxalic acid provides carbamoyl radicals, which are useful for the selective arbamoylation of protonated heteroaromatic bases; this reaction represents the first general and selective method for the N-alkyl or N-arylcarbamoylation of heteroaromatic bases. Compared to alkoxycarbonylation, this reaction is much more effective and selective, owing to more favourable polar and enthalpic effects. The importance of the steric effects is also emphasized.
Three-dimensional electronic scaffold for cardiac applications (2023)

Disclosed here is a three-dimensional electronic scaffold, comprising a porous scaffold and a plurality of micro-strain gauges distributed spatially inside the porous scaffold, wherein the micro-strain gauges are adapted to detect contraction force. Also disclosed is a method comprising detecting and mapping intra-tissue cardiac contraction force of one or more cardiac cells or tissues disposed in a three-dimensional electronic scaffold, wherein the three-dimensional electronic scaffold comprises a porous scaffold and a plurality of micro-strain gauges distributed spatially inside the porous scaffold and in contact with the cardiac cells or tissues, and wherein the micro-strain gauges are adapted to detect contraction force of the cardiac cells or tissues.
Preclinical Development of Pentamidine Analogs Identifies a Potent and Nontoxic Antibiotic Adjuvant (2022)

The difficulty in treating Gram-negative bacteria can largely be attributed to their highly impermeable outer membrane (OM), which serves as a barrier to many otherwise active antibiotics. This can be overcome with the use of perturbant molecules, which disrupt OM integrity and sensitize Gram-negative bacteria to many clinically available Gram-positive-active antibiotics. Although many new perturbants have been identified in recent years, most of these molecules are impeded by toxicity due to the similarities between pathogen and host cell membranes. For example, our group recently reported the cryptic OM-perturbing activity of the antiprotozoal drug pentamidine. Its development as an antibiotic adjuvant is limited, however, by toxicity concerns. Herein, we took a medicinal chemistry approach to develop novel analogs of pentamidine, aiming to improve its OM activity while reducing its off-target toxicity. We identified the compound P35, which induces OM disruption and potentiates Gram-positive-active antibiotics in Acinetobacter baumannii and Klebsiella pneumoniae. Relative to pentamidine, P35 has reduced mammalian cell cytotoxicity and hERG trafficking inhibition. Additionally, P35 outperforms pentamidine in a murine model of A. baumannii bacteremia. Together, this preclinical analysis supports P35 as a promising lead for further development as an OM perturbant.
How to select a replication protocol according to scalability, availability and communication overhead (2002)

Data replication is playing an increasingly important role in the design of parallel information systems. In particular, the widespread use of cluster architectures in high-performance computing has created many opportunities for applying data replication techniques in new areas. For instance, as part of work related to cluster computing in bioinformatics, we have been confronted with the problem of having to choose an optimal replication strategy in terms of scalability, availability and communication overhead. Thus, we have evaluated several representative replication protocols in order to better understand their behavior in practice. The results obtained are surprising in that they challenge many of the assumptions behind existing protocols. Our evaluation indicates that the conventional read-one/write-all approach is the best choice for a large range of applications requiring data replication. We believe this is an important result for anybody developing code for computing clusters as the read-one/write-all strategy is much simpler to implement and more flexible than quorum-based approaches. In this paper we show that, in addition, it is also the best choice using a number of other selection criteria.
Structural and transport properties of Cu/Ta(N)/Cu interfaces in vertical interconnects (2020)

We use first-principles calculations to investigate the structural and transport properties of various Cu/Ta(N)/Cu interface stacks, which are representative of the metal interfaces located at the bottom of vertical interconnects in state-of-the-art back-end-of-line technology. In particular, we consider approximately 2-nm thick layers of several different Ta-based barrier layers sandwiched between two Cu(111) layers, including TaN, α-Ta, β-Ta, and a bilayer TaN/α-Ta structure. Our results highlight that the bilayer Cu/TaN/α-Ta/Cu structure shows both an attractive combination of low electrical resistance and superior dielectric adhesion. We also find that inelastic phonon transport across the interface structures is largely determined by the frequency overlap of the bulk-like phonon density of states of each metal layer. Our results are fed into a simple interconnect performance benchmarking model based on a single-driver signal wire, where we find that metal barrier optimization can result in a net 2.5% stage delay reduction without comprising reliability.
Association Between Duration of SARS-CoV-2 Positivity and Long COVID (2023)

In an observational study, we analyzed 1293 healthcare workers previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), of which 34.1% developed postacute sequelae of SARS-CoV-2 infection (also known as long COVID). Using a multivariate logistic regression model, we demonstrate that the likelihood of developing long COVID in infected individuals rises with the increasing of duration of infection and that 3 doses of the BNT162b2 vaccine are protective, even during the Omicron wave.
ChemInform Abstract: Pyridine Ylide Formation by Capture of Phenylchlorocarbene and tert.‐Butylchlorocarbene. Reaction Rates of an Alkylchlorocarbene by Laser Flash Photolysis. (1988)

Abstract Chlorocarbenes (II) react with pyridine (III) to give ylides (IV) which serve as ideal kinetic probes of carbene dynamics because they are intensely absorbant (480 and 376 nm, resp.) and long lived (τ &gt; 100 μs and ca. 5 μs, respectively).
Identification of a rat liver nuclear protein that binds to the enhancer core element of three animal viruses. (1987)

This report describes the identification and purification of a nuclear protein from rat liver that binds selectively to DNA sequences associated with several animal virus enhancers. The binding activity was tracked by direct DNase I footprinting through four steps of biochemical fractionation. These procedures led to the identification of a polypeptide species exhibiting an apparent molecular weight of 20 kD that accounts for enhancer binding activity. DNase I and dimethyl sulfate footprinting assays were used to examine the manner in which the purified protein binds to enhancer elements associated with SV40, murine sarcoma virus, and polyoma virus. The results of these assays indicate that the initial interaction established between the 20-kD protein and each viral enhancer occurs via a common DNA sequence known as the enhancer core homology.
Flavonoid Baicalein Suppresses Oral Biofilms and Protects Enamel Hardness to Combat Dental Caries (2022)

The objectives of this study were to investigate the effects of a novel method using flavonoids to inhibit Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and dual-species biofilms and to protect enamel hardness in a biofilm-based caries model for the first time. Several flavonoids, including baicalein, naringenin and catechin, were tested. Gold-standard chlorhexidine (CHX) and untreated (UC) groups served as controls. Optimal concentrations were determined by cytotoxicity assay. Biofilm MTT, colony-forming-units (CFUs), biofilm biomass, lactic acid and polysaccharide production were evaluated. Real-time-polymerase-chain reaction (qRT-PCR) was used to determine gene expressions in biofilms. Demineralization of human enamel was induced via S. mutans-C. albicans biofilms, and enamel hardness was measured. Compared to CHX and UC groups, the baicalein group achieved the greatest reduction in S. mutans, C. albicans and S. mutans-C. albicans biofilms, yielding the least metabolic activity, polysaccharide synthesis and lactic acid production (p < 0.05). The biofilm CFU was decreased in baicalein group by 5 logs, 4 logs, 5 logs, for S. mutans, C. albicans and S. mutans-C. albicans biofilms, respectively, compared to UC group. When tested in a S. mutans-C. albicans in vitro caries model, the baicalein group substantially reduced enamel demineralization under biofilms, yielding an enamel hardness that was 2.75 times greater than that of UC group. Hence, the novel baicalein method is promising to inhibit dental caries by reducing biofilm formation and protecting enamel hardness.
Carbon Wonderland from an Engineering Perspective (2018)

The talk will introduce some of the application-driven topics in our group. Applications of graphenic carbon as x-ray transmission windows as well as in DRAM capacitors and diodes will be demonstrated. A novel x-ray transmission window based on graphenic carbon (GC) has been developed and integrated into a silicon drift detector (SDD) with much better performance than beryllium transmission windows that are currently used in the field. It is now used in products from Olympus, Bruker and Oxford. GC integrated on a silicon frame allows for a 7 mm wide window which does not use a mechanical support grid or additional light blocking layers. Compared to beryllium, the novel GC window exhibits an improved x-ray transmission in the important low energy region (0.1 keV - 3 keV) enabling the detection of elements down to carbon while demonstrating excellent mechanical stability, as well as light and vacuum tightness. Be-windows with an opening diameter of 7 mm are specified to withstand a differential pressure of 2 bar. The GC window with a thickness of 1 micrometer exceed this requirement by far. Pressure cycle fatigue for Be-windows is specified to ∼ 20k cycles, while GC has already demonstrated more than 10 million pressure cycles without damage. Therefore, the newly established GC window, can replace beryllium in x-ray transmission windows with a nontoxic and abundant material. Contact resistance and thermal degradation of metal-silicon contacts are challenges in nanoscale CMOS as well as in power device applications. Titanium silicide (TiSi) contacts are commonly used metal-silicon contacts, but are known to diffuse into the active region under high current stress. We show that a graphenic carbon (C) contact to n-type silicon (C-Si) has the same low Schottky barrier height of 0.45 eV as TiSi, but a much improved reliability against high current stress. The C-Si contact is over 100 million times more stable against high current stress pulses than the conventionally used TiSi junction. The C-Si contact properties even show promise to establish an ultra-low, high temperature stable contact resistance. The finding has important consequences for the enhancement of reliability in power devices as well as in Schottky-diodes and electrical contacts to silicon and semiconductors in general (IEDM 2016, IEDM 2018).
Hydroquinone-Induced Depigmentation: Case Report and Review of the Literature (2014)

Melasma is an acquired cutaneous disorder caused by an overproduction of melanin by the enzyme tyrosinase. Melasma remains a therapeutic challenge and no definitive standard therapy exists. Although hydroquinone (HQ) has emerged as the most common treatment, its popularity has recently waned because of concerns about its potential carcinogenicity and manufacturing challenges. The adverse effects of HQ range from the common irritant contact dermatitis to the less frequent exogenous ochronosis (EO). Previous reports suggest that the risk of leukoderma from HQ treatment is limited to individuals of African descent. Herein, we describe for the first time the development of depigmentation and paradoxical hyperpigmentation in 2 patients with Fitzpatrick skin type III/IV after brief treatment of their melasma with the HQ-containing Nu-Derm and Reverse systems.
Early cryptococcal meningitis following treatment with rituximab, fludarabine and cyclophosphamide in a patient with chronic lymphocytic leukemia (2012)

Cryptococcosis is an opportunistic fungal infection, mainly reported in patients with acquired immune deficiency syndrome (AIDS), more rarely encountered in highly immunocompromised patients with h...
J2410104 Novel measurement technique of mattress deformation for the validation of biomechanical simulation (2015)

In this study, the method to measure the deformation at the surface and inside of a mattress was developed. The mattress with contrast media on and in it was manufactured, and the manikin in imination of the shape of the human trunk, of which the weight was equivalent to the human one, was manufactured by photo fabrication. The mattress with the manikin on it were photographed by X-ray CT. It was confirmed that the CT images had the phantom of contrast media and the mattress deformation state could be visualized. The coordinates of positions equivalent to the centers of gravity of contrast media were acquired from image processing. This process enabled us that deformation state of the mattress was evaluated using numerical values. The plane shape at the mattress surface contacting the manikin was almost the same as the shape of the manikin. Thus, the digitizing precision of our method was estimated by comparing the shape of the manikin with the digitized result, showing the precision was about 2.4mm.
Implantation methodology development for tissue-engineered-electronic-neural-interface (TEENI) devices (2017)

Regenerative peripheral-nerve interfaces are a novel method for integrating with the peripheral nervous system. These devices have the potential to isolate and transduce both afferent (sensory) and efferent (motor) neural signals to produce fine control of advanced prosthetics. We have developed a novel regenerative device comprised of microfabricated polyimide electrode threads supported by a hydrogel scaffold containing methacrylated hyaluronic acid, collagen I, and laminin to enable intimate contact with regenerating axons. While this advanced device holds theoretical promise for establishing a stable chronic neural interface, it also requires a novel surgical approach in comparison to current existing methods of peripheral neural interface technologies. Here we describe the development of the surgical methodology required for successful chronic implantation of the TEENI device in the rat sciatic nerve.
Abstract 1683: Autophagy inhibition for cancer therapy. (2013)

Abstract In tumor but not normal cells, the stress-inducible heat shock protein 70 (HSP70) is abundantly expressed and becomes incorporated into lysosome membranes, where it serves to stabilize and protect lysosome function. Inhibition of HSP70 thus results in defective lysosome function, along with impaired autophagy. We previously reported that the HSP70 inhibitor phenylethynesulfonamide (PES) is a potent and effective autophagy inhibitor (1). PES shows marked cytotoxicity to tumor cells, but minimal effects in normal, non-transformed cells. We previously reported that PES binds to both HSP70 and to the constitutively-expressed family member HSC70; these are critical co-chaperones for HSP90, and we previously reported that treatment of tumor cells with PES leads to decreased function of HSP90 client proteins like HER2, AKT and CDK4 (2). We have recently performed a preliminary structure-activity relationship for PES. These studies revealed a novel PES analogue that we call PES-Cl, which shows 10-fold decreased IC50 for tumor cells, minimal cytotoxicity to normal cells, and a greatly enhanced ability to inhibit autophagy. In vitro we show that PES-Cl is cytotoxic to melanoma cells, including those with both intrinsic and acquired resistance to BRAF inhibitors, but shows minimal cytotoxicity to primary melanocytes. In a pre-clinical model for B-cell lymphoma (Eu-myc transgenic mouse), we show that PES-Cl demonstrates significant ability to extend the life of mice (p=0.000006), with no evidence for liver pathology or toxicity. We report that PES binds to the substrate-binding domain of HSP70, and requires the C-terminal helical ‘lid’ of this protein (amino acids 573-616) in order to bind. Using molecular modeling and in silico docking, we have identified a candidate binding site for PES in HSP70, and we identify point mutants that fail to interact with this compound. Our cell cycle analyses of PES-Cl-treated cells show that this compound induces G2/M arrest. Interestingly, we also show that this HSP70 inhibitor impairs the activity of the Anaphase Promoting Complex/Cyclosome (APC/C) in cell-free extracts. PES-Cl is thus a promising new HSP70 inhibitor that binds to the C-terminal ‘lid’ of HSP70, and multiple mechanisms of action: inhibition of autophagy, inhibition of HSP90 function, and inhibition of the Anaphase Promoting Complex/Cyclosome (APC/C). 1. Leu et al, Molecular Cell, 6(1):15-27, 2009 2. Leu et al, Molecular Cancer Research, 9(7):936-47, 2011 Citation Format: Gregor Balaburski, Julia I-Ju Leu, Neil Beeharry, Seth Hayik, Mark D. Andrake, Gao Zhang, Meenhard Herlyn, Jessie Villanueva, Roland L. Dunbrack, Tim Yen, Donna L. George, Maureen E. Murphy. Autophagy inhibition for cancer therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1683. doi:10.1158/1538-7445.AM2013-1683
Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots” (2005)

Crossover (CO) is a key process for the accurate segregation of homologous chromosomes during the first meiotic division. In most eukaryotes, meiotic recombination is not homogeneous along the chromosomes, suggesting a tight control of the location of recombination events. We genotyped 71 single nucleotide polymorphisms (SNPs) covering the entire chromosome 4 of Arabidopsis thaliana on 702 F2 plants, representing 1404 meioses and allowing the detection of 1171 COs, to study CO localization in a higher plant. The genetic recombination rates varied along the chromosome from 0 cM/Mb near the centromere to 20 cM/Mb on the short arm next to the NOR region, with a chromosome average of 4.6 cM/Mb. Principal component analysis showed that CO rates negatively correlate with the G+C content (P = 3x10(-4)), in contrast to that reported in other eukaryotes. COs also significantly correlate with the density of single repeats and the CpG ratio, but not with genes, pseudogenes, transposable elements, or dispersed repeats. Chromosome 4 has, on average, 1.6 COs per meiosis, and these COs are subjected to interference. A detailed analysis of several regions having high CO rates revealed "hot spots" of meiotic recombination contained in small fragments of a few kilobases. Both the intensity and the density of these hot spots explain the variation of CO rates along the chromosome.
Algorithm Negotiation in DNSSEC (2018)

This document specifies a DNS extension that allows a DNS client to
specify a list of DNSSEC algorithms, in preference order, that the
client desires to use. A DNS server upon receipt of this extension can
choose to selectively respond with DNSSEC signatures using the most
preferred algorithm they support. This mechanism may make it easier
for DNS zone operators to support signing zone data simultaneously
with multiple DNSSEC algorithms, without significantly increasing the
size of DNS responses. It will also allow an easier way to transition
to new algorithms while still retaining support for older DNS
validators that do not yet support the new algorithms.