gebhart/patrepeval huggingface dataset:
From Iron and Cysteine to Iron-Sulfur Clusters: the Biogenesis Protein Machineries (2008)

This review describes the two main systems, namely the Isc (iron-sulfur cluster) and Suf (sulfur assimilation) systems, utilized by Escherichia coli and Salmonella for the biosynthesis of iron-sulfur (Fe-S) clusters, as well as other proteins presumably participating in this process. In the case of Fe-S cluster biosynthesis, it is assumed that the sulfur atoms from the cysteine desulfurase end up at cysteine residues of the scaffold protein, presumably waiting for iron atoms for cluster assembly. The review discusses the various potential iron donor proteins. For in vitro experiments, in general, ferrous salts are used during the assembly of Fe-S clusters, even though this approach is unlikely to reflect the physiological conditions. The fact that sulfur atoms can be directly transferred from cysteine desulfurases to scaffold proteins supports a mechanism in which the latter bind sulfur atoms first and iron atoms afterwards. In E. coli, fdx gene inactivation results in a reduced growth rate and reduced Fe-S enzyme activities. Interestingly, the SufE structure resembles that of IscU, strengthening the notion that the two proteins share the property of acting as acceptors of sulfur atoms provided by cysteine desulfurases. Several other factors have been suggested to participate in cluster assembly and repair in E. coli and Salmonella. Most of them were identified by their abilities to act as extragenic and/or multicopy suppressors of mutations in Fe-S cluster metabolism, while others possess biochemical properties that are consistent with a role in Fe-S cluster biogenesis.
Genetic ablation of cyclophilin D rescues mitochondrial defects and prevents muscle apoptosis in collagen VI myopathic mice (2009)

Ullrich congenital muscular dystrophy (UCMD) and Bethlem myopathy are inherited muscle disorders caused by mutations of genes encoding the extracellular matrix protein collagen VI (ColVI). Mice lacking ColVI (Col6a1(-/-)) display a myopathic phenotype associated with ultrastructural alterations of mitochondria and sarcoplasmic reticulum, mitochondrial dysfunction with abnormal opening of the permeability transition pore (PTP) and increased apoptosis of muscle fibers. Treatment with cyclosporin (Cs) A, a drug that desensitizes the PTP by binding to cyclophilin (Cyp)-D, was shown to rescue myofiber alterations in Col6a1(-/-) mice and in UCMD patients, suggesting a correlation between PTP opening and pathogenesis of ColVI muscular dystrophies. Here, we show that inactivation of the gene encoding for Cyp-D rescues the disease phenotype of ColVI deficiency. In the absence of Cyp-D, Col6a1(-/-) mice show negligible myofiber degeneration, rescue from mitochondrial dysfunction and ultrastructural defects, and normalized incidence of apoptosis. These findings (i) demonstrate that lack of Cyp-D is equivalent to its inhibition with CsA at curing the mouse dystrophic phenotype; (ii) establish a cause-effect relationship between Cyp-D-dependent PTP regulation and pathogenesis of the ColVI muscular dystrophy and (iii) validate Cyp-D and the PTP as pharmacological targets for the therapy of human ColVI myopathies.
Impact of Blood Sugar Control on Metabolites and Carbohydrate Metabolism in Type 1 Diabetes (2018)

In type 1 diabetes (T1D), long-term blood sugar control measured by HbA1c can vary over a wide range. Although metabolites are commonly studied in type 2 diabetes (T2D) as they relate to HbA1c, similar studies in T1D are few. Since the underlying etiologies of T1D and T2D are different, we explored the overall pathways of metabolism in T1D subjects with tight vs. poor blood sugar control. T1D subjects (n=50) were divided into two groups (n=25 each) based on low vs. high HbA1c (Screen 1, low: mean 6.7 ± 0.1%; high: mean 8.7 ± 0.3%). Serum samples were analyzed on a metabolomic GC/HPLC/MS platform and analyzed for differences in biochemicals between the groups. The screen was repeated with a second group of 50 patients for verification (Screen 2, mean 6.3 ± 0.1%; mean 8.0 ± 0.2%) and then both screens combined. For each detected biochemical, average scaled intensity was determined and statistical significance of differences was calculated using a two-tailed, unpaired Student’s T test (p-values) and False Discovery Rate (q-values). The platform distinguished 690 components in Screen 1 and 623 biochemicals in Screen 2. In Screen 1, two biochemicals, including glucose, showed significant differences (≦0.05) for both p and q value. In Screen 2, none of the biochemicals reached threshold. When the screens were combined (100 samples), 10 biochemicals were significant for both p and q. Three components (glucose, mannose and 1,5-AG) were carbohydrates related to blood sugar control and thus expected in a high and low HbA1c analysis. Significant biochemicals commonly found in T2D and related to blood sugar control were not significant in T1D for both p and q in the screens. We conclude that few metabolites are correlated in T1D with tight vs. poor blood sugar control compared to T2D. Unlike T2D, metabolites related to intracellular sugar utilization, the Krebs cycle and purine synthesis are unrelated to blood sugar control in T1D cohorts. Disclosure W. Kuhtreiber: None. S.E. Janes: None. M.W. Yang: None. D.L. Faustman: None.
Metro ring node module based on polymeric planar lightwave circuits (2004)

We describe a 4-channel metro ring node module that performs add/drop, protection switching, and power equalization functionalities on a single chip. The worst-case insertion loss is 1.25 dB.
Quantum Feature Extraction for THz Multi-Layer Imaging (2022)

A learning-based THz multi-layer imaging has been recently used for contactless three-dimensional (3D) positioning and encoding. We show a proof-of-concept demonstration of an emerging quantum machine learning (QML) framework to deal with depth variation, shadow effect, and double-sided content recognition, through an experimental validation.
Subir Kumar Ghosh (1932-2008) (2009)

doyen of modern structural geology, breathed his last on 30 October, 2008 after a massive heart attack.Though he was seriously ill for the last five years, his death came as a great shock.He was not only my teacher, but also my friend, philosopher and guide for more than 40 years.He initiated the modern trend in structural geology in the country by combining experimental and mathematical models with detailed field studies.In a span of fifty years of research, he has covered a wide spectrum of topics in structural geology and made significant contributions in each of them.The scientific work of a person is judged not by the number of papers but by the impact of his research on the subject as a whole.Ghosh's research was able to create that kind of enduring impact on the subjects he dealt with.For this reason, he was much admired by fellow researchers from all over the world.
Dynamic Channel Emulation in a Cost-Effective MPAC Setup for mmWave Devices Over-The-Air Testing with Dominant Cluster Concept (2020)

Millimeter-Wave (mmWave) has been considered as the key enabler for the fifth generation (5G) communications. The link budget and spectral efficiency of mmWave communications can be further enhanced by adopting the massive multiple-input-multiple-output (MIMO) exploiting beamforming. Nevertheless, it is essential to design and test mmWave 5G devices under various realistic scenarios, since the uncontrollable radio propagation channels pose intrinsic limitations on system performance. This requires emulating the realistic dynamic mmWave channels in a reproducible manner in laboratories, hence the goal of this paper. In this contribution, the beamforming effect is firstly investigated, showing that the non-dominant clusters existing in the mmWave channels are insignificant with beamforming operations applied in mmWave 5G devices. Thus, an over-the-air (OTA) emulation strategy for dynamic mmWave channels is then proposed based on a dominant-cluster concept using a sectored multiprobe anechoic chamber (SMPAC) setup. The key design parameters including the probe number and the angular spacing of probes are investigated through comprehensive simulations. A cost-effective switch circuit is also designed for this purpose and validated in the simulation. Furthermore, a dynamic mmWave channel measured in an indoor scenario at 28-30 GHz is presented, where the proposed emulation strategy is also validated by reproducing the measured reality.
Lightweight Materials for Automotive Applications: Final Report CRADA No. TC-296-92-C (2000)

This project was concerned with low cost, metal matrix composites for chassis and powertrain applications. The project had two major components - fatigue and non-destructive evaluation (NDE). The fatigue component of the project studied the fatigue failure mechanisms at elevated temperature (both isothermal and thermo-mechanical fatigue) with the objective of improving material performance. The NDE component of the project developed rapid, high resolution NDE techniques to quantify internal defects in components. All deliverables for the project were met with the exception of transfer of an NDE inspection system. There were no significant changes in either the fatigue or the NDE portions of the project relative to the original proposal.
Real-time redundancy allocation for time-varying underwater acoustic channels (2012)

In this paper, we jointly address reliability and spectral efficiency in underwater acoustic (UWA) communications by proposing optimal redundancy allocation over time-varying conditions in a communication link. To do so, we use recent results on tight approximation of codeword error probability in the finite block-length regime. First, we propose and evaluate an optimization framework. Then, we design a real-time algorithm, able to allocate the redundancy in a point-to-point link, without adding control messages. We evaluate the performance of the proposed algorithm by considering both rapidly and slowly time-varying experimental channel conditions. Finally, we compare the performance of our algorithm with that obtained with constant length codewords. Results show that the proposed redundancy allocation scheme is more efficient than constant allocation schemes under different channel conditions.
K336I mutant actin alters the structure of neighbouring protomers in filaments and reduces affinity for actin-binding proteins (2019)

Mutation of the Lys-336 residue of actin to Ile (K336I) or Asp (K336E) causes congenital myopathy. To understand the effect of this mutation on the function of actin filaments and gain insight into the mechanism of disease onset, we prepared and biochemically characterised K336I mutant actin from Dictyostelium discoideum. Subtilisin cleavage assays revealed that the structure of the DNase-I binding loop (D-loop) of monomeric K336I actin, which would face the adjacent actin-protomer in filaments, differed from that of wild type (WT) actin. Although K336I actin underwent normal salt-dependent reversible polymerisation and formed apparently normal filaments, interactions of K336I filaments with alpha-actinin, myosin II, and cofilin were disrupted. Furthermore, co-filaments of K336I and WT actins also exhibited abnormal interactions with cofilin, implying that K336I actin altered the structure of the neighbouring WT actin protomers such that interaction between cofilin and the WT actin protomers was prevented. We speculate that disruption of the interactions between co-filaments and actin-binding proteins is the primary reason why the K336I mutation induces muscle disease in a dominant fashion.
SP2 system architecture (1999)

Scalable parallel systems are increasingly being used today to address existing and emerging application areas that require performance levels significantly beyond what symmetric multiprocessors are capable of providing. These areas include traditional technical computing applications, commercial computing applications such as decision support and transaction processing, and emerging areas such as “grand challenge” applications, digital libraries, and video production and distribution. The IBM SP2™ is a general-purpose scalable parallel system designed to address a wide range of these applications. This paper gives an overview of the architecture and structure of SP2, discusses the rationale for the significant system design decisions that were made, indicates the extent to which key objectives were met, and identifies future system challenges and advanced technology development areas.
Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Casual Genes and Mutations on Pig Chromosome 17 (2011)

The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining.
New 2‐phenyl‐4,5,6,7‐tetrahydro‐2H‐indazole derivatives as paddy field herbicides (2004)

A series of 3-chloro-2-(4-chloro-2-fluorophenyl)-4,5,6,7-tetrahydro-2H-indazole derivatives containing various substituted isoxazolinylmethoxy groups at the 5-position of the benzene ring were synthesized and their herbicidal activities assessed under greenhouse and flooded paddy conditions. Among them, compounds having a phenyl or cyano substituent at the 3-position of the 5-methyl-isoxazolin-5-yl structure demonstrated good rice selectivity and potent herbicidal activity against annual weeds at 16-63 g AI ha(-1) under greenhouse conditions. Field trials indicated that these two compounds controlled a wide range of annual weeds rapidly with a good tolerance on transplanted rice seedlings by pre-emergence application. They showed a low mammalian and environmental toxicity in various toxicological tests.
Developmental regulation of glucosidase I, an enzyme involved in the processing of asparagine-linked glycoproteins in rat mammary gland. (1990)

Glucosidase I involved in the processing of N-linked glycoproteins was purified to homogeneity from the lactating rat mammary gland. The purified enzyme exhibited a single band at 85 kDa on 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. Polyclonal antibodies raised against the enzyme recognized a similar band on Western blots and also inhibited the enzyme activity. The enzyme levels gradually increased until the midlactation stage and thereafter declined sharply during the period of postlactation. A similar profile of the levels of immunoreactive glucosidase I was observed. These findings suggest that the accumulation of glucosidase I is modulated as a function of gland ontogeny. The results on hormonal regulation of glucosidase I indicate that the synthesis of the enzyme is stimulated by a combination of insulin, hydrocortisone, and prolactin; additionally, epidermal growth factor may play a role in this regulation. The above observation was substantiated by immunoprecipitation of [35S]methionine-labeled microsomal extracts with anti-glucosidase I antibodies. The immunoprecipitation of soluble extracts from [35S]methionine-labeled tissue with anti-rat alpha-lactalbumin antibodies indicates that these hormones not only stimulate the synthesis of alpha-lactalbumin but also play an important role in its glycosylation.
From RTL to CUDA: A GPU Acceleration Flow for RTL Simulation with Batch Stimulus (2022)

High-throughput RTL simulation is critical for verifying today’s highly complex SoCs. Recent research has explored accelerating RTL simulation by leveraging event-driven approaches or partitioning heuristics to speed up simulation on a single stimulus. To further accelerate throughput performance, industry-quality functional verification signoff must explore running multiple stimulus (i.e., batch stimulus) simultaneously, either with directed tests or random inputs. In this paper, we propose RTLFlow, a GPU-accelerated RTL simulation flow with batch stimulus. RTLflow first transpiles RTL into CUDA kernels that each simulates a partition of the RTL simultaneously across multiple stimulus. It also leverages CUDA Graph and pipeline scheduling for efficient runtime execution. Measuring experimental results on a large industrial design (NVDLA) with 65536 stimulus, we show that RTLflow running on a single A6000 GPU can achieve a 40 × runtime speed-up when compared to an 80-thread multi-core CPU baseline.
Intrinsic chemosensitivity of rostral ventrolateral medullary sympathetic premotor neurons in the in situ arterially perfused preparation of rats (2014)

Brainstem hypoperfusion is a major excitant of sympathetic activity triggering hypertension, but the exact mechanisms involved remain incompletely understood. A major source of excitatory drive to preganglionic sympathetic neurons originates from the ongoing activity of premotor neurons in the rostral ventrolateral medulla (RVLM sympathetic premotor neurons). The chemosensitivity profile of physiologically characterized RVLM sympathetic premotor neurons during hypoxia and hypercapnia remains unclear. We examined whether physiologically characterized RVLM sympathetic premotor neurons can sense brainstem ischaemia intrinsically. We addressed this issue in a unique in situ arterially perfused preparation before and after a complete blockade of fast excitatory and inhibitory synaptic transmission. During hypercapnic hypoxia, respiratory modulation of RVLM sympathetic premotor neurons was lost, but tonic firing of most RVLM sympathetic premotor neurons was elevated. After blockade of fast excitatory and inhibitory synaptic transmission, RVLM sympathetic premotor neurons continued to fire and exhibited an excitatory firing response to hypoxia but not hypercapnia. This study suggests that RVLM sympathetic premotor neurons can sustain high levels of neuronal discharge when oxygen is scarce. The intrinsic ability of RVLM sympathetic premotor neurons to maintain responsivity to brainstem hypoxia is an important mechanism ensuring adequate arterial pressure, essential for maintaining cerebral perfusion in the face of depressed ventilation and/or high cerebral vascular resistance.
Sorption of Lead Ions on ZIF-8 and ZIF-67 Zeolite-Like Imidazolate Frameworks and Calcium Alginate Composites (2022)

Composites are synthesized on the basis of ZIF-8 and ZIF-67 zeolite-like imidazolate frameworks and calcium alginate (ZIF-8@CA and ZIF-67@CA). The adsorption capacity, degree of removal, and kinetics of sorption are studied for all sorbents using lead ions as an example. There is a synergistic effect between the ZIF-8 zeolite-like framework and calcium alginate providing an increased sorption capacity of the resulting composites with respect to lead ions and higher hydrolytic stability of the ZIF-67 composite with calcium alginate.
Physics of liquid crystals of bent-shaped molecules (2018)

Bent-shaped molecules form a large variety of liquid crystal phases, such as nematic and smectic phases with polar and even chiral order, and also the recently discovered twist-bend nematic phase with a heliconical modulation of the nematic director. A small kink in the molecular shape can lead to new properties and liquid crystal phases. This paper discusses the theory of liquid crystals of banana-shaped molecules and the underlying physics, and it reviews experimental research of both rigid and flexible bent-core molecules.
p38 MAP kinase is a therapeutic target for hepatic encephalopathy in rats with portacaval shunts (2011)

These findings suggest that reducing neuroinflammation by using inhibitors of p38 would improve the neurological status in HE without inducing secondary effects in the kidney.
Test of the universality of τ and μ lepton couplings in W-boson decays with the ATLAS detector (2021)

Abstract The standard model of particle physics encapsulates our best current understanding of physics at the smallest scales. A fundamental axiom of this theory is the universality of the couplings of the different generations of leptons to the electroweak gauge bosons. The measurement of the ratio of the decay rate of W bosons to τ leptons and muons, R ( τ / μ ), constitutes an important test of this axiom. Using 139 fb −1 of proton–proton collisions recorded with the ATLAS detector at a centre-of-mass energy of 13 TeV, we report a measurement of this quantity from di-leptonic $$t\overline{t}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>t</mml:mi> <mml:mover> <mml:mrow> <mml:mi>t</mml:mi> </mml:mrow> <mml:mo>¯</mml:mo> </mml:mover> </mml:mrow> </mml:math> events where the top quarks decay into a W boson and a bottom quark. We can distinguish muons originating from W bosons and those originating from an intermediate τ lepton through the muon transverse impact parameter and differences in the muon transverse momentum spectra. The measured value of R ( τ / μ ) is 0.992 ± 0.013 [± 0.007(stat) ± 0.011(syst)] and is in agreement with the hypothesis of universal lepton couplings as postulated in the standard model. This is the only such measurement from the Large Hadron Collider, so far, and obtains twice the precision of previous measurements.
Mixed-Initiative Approaches to Global Editing in Slideware (2015)

Good alignment and repetition of objects across presentation slides can facilitate visual processing and contribute to audience understanding. However, creating and maintaining such consistency during slide design is difficult. To solve this problem, we present two complementary tools: (1) StyleSnap, which increases the alignment and repetition of objects by adaptively clustering object edge positions and allowing parallel editing of all objects snapped to the same spatial extent; and (2) FlashFormat, which infers the least-general generalization of editing examples and applies it throughout the selected range. In user studies of repetitive styling task performance, StyleSnap and FlashFormat were 4-5 times and 2-3 times faster respectively than conventional editing. Both use a mixed-initiative approach to improve the consistency of slide decks and generalize to any situations involving direct editing across disjoint visual spaces.
Weyl Points in Three-Dimensional Optical Lattices: Synthetic Magnetic Monopoles in Momentum Space (2015)

We show that a Hamiltonian with Weyl points can be realized for ultracold atoms using laser-assisted tunneling in three-dimensional optical lattices. Weyl points are synthetic magnetic monopoles that exhibit a robust, three-dimensional linear dispersion, identical to the energy-momentum relation for relativistic Weyl fermions, which are not yet discovered in particle physics. Weyl semimetals are a promising new avenue in condensed matter physics due to their unusual properties such as the topologically protected "Fermi arc" surface states. However, experiments on Weyl points are highly elusive. We show that this elusive goal is well within experimental reach with an extension of techniques recently used in ultracold gases.