gebhart/patrepeval huggingface dataset:
Isolation of bacteriophages specific for the K1 polysaccharide antigen of Escherichia coli (1977)

Five bacteriophage stocks were prepared after enrichment of a sewage sample using Escherichia coli 02:K1:H4 (strain U9/41). The bacteriophages were tested for their ability to lyse 224 strains of E. coli that had been tested for the presence of the K1 antigen by means of an antiserum-agar diffusion technique, using a meningococcus group B antiserum known to detect the E. coli K1 antigen. The standard test strains for E. coli K antigens 2 to 99 were used as control strains. Of the 101 strains found to possess the K1 antigen using the antiserum-agar technique, 93 were lysed by at least one of the bacteriophages, whereas 8 of the 123 strains apparently lacking K1 were lysed by one or more of the bacteriophages. None of the standard test strains for K antigens 2 to 99 was lysed by any of the bacteriophages. The eight strains thought to lack K1 but that were lysed by bacteriophage were re-examined by immunoelectrophoresis, using meningococcus group B antiserum; five of the eight strains gave a precipitin line corresponding to K1. The use of K1-specific bacteriophages offers an inexpensive and easy method for the identification of the K1 antigen.
LEGS: Learning Efficient Grasp Sets for Exploratory Grasping (2022)

While deep learning has enabled significant progress in designing general purpose robot grasping systems, there remain objects which still pose challenges for these systems. Recent work on Exploratory Grasping has formalized the problem of systematically exploring grasps on these adversarial objects and explored a multi-armed bandit model for identifying high-quality grasps on each object stable pose. However, these systems are still limited to exploring a small number or grasps on each object. We present Learned Efficient Grasp Sets (LEGS), an algorithm that efficiently explores thousands of possible grasps by maintaining small active sets of promising grasps and determining when it can stop exploring the object with high confidence. Experiments suggest that LEGS can identify a high-quality grasp more efficiently than prior algorithms which do not use active sets. In simulation experiments, we measure the gap between the success probability of the best grasp identified by LEGS, baselines, and the most-robust grasp (verified ground truth). After 3000 exploration steps, LEGS outperforms baseline algorithms on 10/14 and 25/39 objects on the Dex-Net Adversarial and EGAD! datasets respectively. We then evaluate LEGS in physical experiments; trials on 3 challenging objects suggest that LEGS converges to high-performing grasps significantly faster than baselines. See https://sites.google.com/view/LEGS-exp-grasping for supplemental material and videos.
Magnetic phase transition in single crystals of the chiral helimagnet Cr1/3NbS2 (2013)

The chiral helimagnet Cr${}_{1/3}$NbS${}_{2}$ has been investigated by magnetic, transport, and thermal properties measurements on single crystals and by first-principles electronic structure calculations. From the measured field and temperature dependence of the magnetization for fields applied perpendicular to the $c$ axis, the magnetic phase diagram has been constructed in the vicinity of the phase transition. A transition from a paramagnetic to a magnetically ordered phase occurs near 120 K. The transition is found to strongly affect the electrical transport. The resistivity decreases sharply upon cooling near 120 K, and the spin reorientation from the helimagnetic ground state to the commensurate ferromagnetic state is evident in the magnetoresistance. At high fields, a large magnetoresistance ($55%$ at 140 kOe) is observed near the magnetic transition temperature. Heat capacity and electronic structure calculations show that the density of states at the Fermi level is low in the magnetically ordered state.
Statut scolaire et image de soi en fin de primaire : étude clinique de la représentation par l'enfant de son niveau et de ses inférences sur sa scolarité (2004)

Dans toute classe il existe une distribution implicite des eleves : les bons, les moyens, les faibles. Le statut scolaire est attribue par les enseignants. Mais selon les pratiques pedagogiques, il est plus ou moins communique aux enfants qui en ont une representation. Cette image de soi peut primer sur le jugement professoral. Ces decalages sont alors plus ou moins importants, les plus couramment reperes etant ceux qui ne s'effectuent que d'un cran, les plus rares etant ceux a deux crans (un bon qui se juge moyen ou faible). Ces illusions perceptives sont evolutives, elles depassent la simple representation de l'eleve, sont en lien avec l'image de soi que se construit l'enfant selon son parcours de vie et sont le temoignage d'une aptitude a reagir face a un statut impose. Quelles en sont les repercussions sur les resultats scolaires ? Se declarer en decalage n'est-ce pas une sorte de levier de resilience, permettant a certains de rebondir, a d'autres de regresser ?
Structural Analysis of the SiCGe Epitaxial Layer Grown on SiC Substrate (2016)

Growth of SiCGe ternary alloy on 6H-SiC in a conventional hot-wall CVD system was studied，and the ternary alloy films were characterized by means of SEM，EDS and PL. It has been found that the samples grown at a narrow temperature
region exhibit a two-phase co-growth aspect，which consists of arelatively smooth background region and some randomly distributed sphericalislands.Materials in the two phases were found to have different compositions by EDS. The islands is a Ge-rich material with Ge content of more than 40％, while the Ge content of background iS less than 1％. SEM images show that the two materials seem to have different growth rates and the background seems to be a defect-rich region，where a high density of stacking faults is evident.The PL peaks located at 2.2eV and 2.7eV come from the interband radiative recombination of the islands and background region, respectively.
Investigations of the impact of altered auditory feedback in-the-ear devices on the speech of people who stutter: One-year follow-up (2006)

These findings support the notion that a device delivering AAF is a viable therapeutic alternative in the treatment of stuttering.
CoDisasm (2015)

Fighting malware involves analyzing large numbers of suspicious binary files. In this context, disassembly is a crucial task in malware analysis and reverse engineering. It involves the recovery of assembly instructions from binary machine code. Correct disassembly of binaries is necessary to produce a higher level representation of the code and thus allow the analysis to develop high-level understanding of its behavior and purpose. Nonetheless, it can be problematic in the case of malicious code, as malware writers often employ techniques to thwart correct disassembly by standard tools. In this paper, we focus on the disassembly of x86 self-modifying binaries with overlapping instructions. Current state-of-the-art disassemblers fail to interpret these two common forms of obfuscation, causing an incorrect disassembly of large parts of the input. We introduce a novel disassembly method, called concatic disassembly, that combines CONCrete path execution with stATIC disassembly. We have developed a standalone disassembler called CoDisasm that implements this approach.
IGV GmbH Experience Report, Industrial Production of Microalgae Under Controlled Conditions: Innovative Prospects (2013)

The experience report on closed photobioreactor (PBR) developments at IGV Biotech during the last 30 years presents a review of successful and, in our experience, failed technical and technological developments. Finally, the glass-tube-type PBRs, created and continuously improved by IGV, achieved a worldwide application both in laboratories and in industrial production. This type of PBR is prominent because of cost levels feasible for the production of high-value products, but not for CO2 capture and fuel production as is the present trend in microalgal biotechnology. In terms of a future outlook, especially for this field, ideas and results for ultrathin-layer PBRs are presented, which are promising enough for strong efforts in technological development.
A Ratiometric Calcium Reporter CGf Reveals Calcium Dynamics Both in the Single Cell and Whole Plant Levels Under Heat Stress (2021)

Land plants evolved to quickly sense and adapt to temperature changes, such as hot days and cold nights. Given that calcium (Ca<sup>2+</sup>) signaling networks are implicated in most abiotic stress responses, heat-triggered changes in cytosolic Ca<sup>2+</sup> were investigated in <i>Arabidopsis</i> leaves and pollen. Plants were engineered with a reporter called CGf, a ratiometric, genetically encoded Ca<sup>2+</sup> reporter with an m<b>C</b>herry reference domain fused to an intensiometric Ca<sup>2+</sup> reporter <b>G</b>CaMP6<b>f</b>. Relative changes in [Ca<sup>2+</sup>]<sub>cyt</sub> were estimated based on CGf's apparent <i>K</i> <sub>D</sub> around 220 nM. The ratiometric output provided an opportunity to compare Ca<sup>2+</sup> dynamics between different tissues, cell types, or subcellular locations. In leaves, CGf detected heat-triggered cytosolic Ca<sup>2+</sup> signals, comprised of three different signatures showing similarly rapid rates of Ca<sup>2+</sup> influx followed by differing rates of efflux (50% durations ranging from 5 to 19 min). These heat-triggered Ca<sup>2+</sup> signals were approximately 1.5-fold greater in magnitude than blue light-triggered signals in the same leaves. In contrast, growing pollen tubes showed two different heat-triggered responses. Exposure to heat caused tip-focused steady growth [Ca<sup>2+</sup>]<sub>cyt</sub> oscillations to shift to a pattern characteristic of a growth arrest (22%), or an almost undetectable [Ca<sup>2+</sup>]<sub>cyt</sub> (78%). Together, these contrasting examples of heat-triggered Ca<sup>2+</sup> responses in leaves and pollen highlight the diversity of Ca<sup>2+</sup> signals in plants, inviting speculations about their differing kinetic features and biological functions.
Hydrogen activation by [NiFe]-hydrogenases (2016)

Hydrogenase-1 (Hyd-1) from Escherichia coli is a membrane-bound enzyme that catalyses the reversible oxidation of molecular H2 The active site contains one Fe and one Ni atom and several conserved amino acids including an arginine (Arg(509)), which interacts with two conserved aspartate residues (Asp(118) and Asp(574)) forming an outer shell canopy over the metals. There is also a highly conserved glutamate (Glu(28)) positioned on the opposite side of the active site to the canopy. The mechanism of hydrogen activation has been dissected by site-directed mutagenesis to identify the catalytic base responsible for splitting molecular hydrogen and possible proton transfer pathways to/from the active site. Previous reported attempts to mutate residues in the canopy were unsuccessful, leading to an assumption of a purely structural role. Recent discoveries, however, suggest a catalytic requirement, for example replacing the arginine with lysine (R509K) leaves the structure virtually unchanged, but catalytic activity falls by more than 100-fold. Variants containing amino acid substitutions at either or both, aspartates retain significant activity. We now propose a new mechanism: heterolytic H2 cleavage is via a mechanism akin to that of a frustrated Lewis pair (FLP), where H2 is polarized by simultaneous binding to the metal(s) (the acid) and a nitrogen from Arg(509) (the base).
Leiomyosarcoma of the urinary bladder: a clinicopathological study of 34 cases (2010)

The authors conclude that LMS-UB occurs in older adults of either sex and is characterised by aggressive behaviour, with adverse outcome in >60% of cases. Certain advantages of the FNCLCC system may support its more widespread adoption for future studies.
The blueprints of power (1998)

Watson, J.; Downey (1998). The blueprints of power. Banda aparte. (12):65-68. http://hdl.handle.net/10251/42291.
Thermal impedance of ceramic packages using beam-Lead IC chips (1968)

An integrated circuit package utilizing beam-lead sealed junction (BLSJ) silicon chips either singly or in multiple arrays consists of a ceramic (99.5% Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> ) substrate with a thin film metallic conductor pattern. The beam-leaded chip (or chips) is thermocompression bonded to the metallizing pattern and coated with a silicone resin for protection from humidity and surface contamination. External leads are also TC bonded to the metallizing pattern for connection to the outside world.
Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp. (2023)

In nature, chitin, the most abundant marine biopolymer, does not accumulate due to the action of chitinolytic organisms, whose saccharification systems provide instructional blueprints for effective chitin conversion. Therefore, discovery and deconstruction of chitinolytic machineries and associated enzyme systems are essential for the advancement of biotechnological chitin valorization. Through combined investigation of the chitin-induced secretome with differential proteomic and transcriptomic analyses, a holistic system biology approach has been applied to unravel the chitin response mechanisms in the Gram-negative <i>Jeongeupia wiesaeckerbachi</i>. Hereby, the majority of the genome-encoded chitinolytic machinery, consisting of various glycoside hydrolases and a lytic polysaccharide monooxygenase, could be detected extracellularly. Intracellular proteomics revealed a distinct translation pattern with significant upregulation of glucosamine transport, metabolism, and chemotaxis-associated proteins. While the differential transcriptomic results suggested the overall recruitment of more genes during chitin metabolism compared to that of glucose, the detected protein-mRNA correlation was low. As one of the first studies of its kind, the involvement of over 350 unique enzymes and 570 unique genes in the catabolic chitin response of a Gram-negative bacterium could be identified through a three-way systems biology approach. Based on the cumulative data, a holistic model for the chitinolytic machinery of <i>Jeongeupia</i> spp. is proposed.
Design procedures for submarine-deployable bistatic sonar systems (1984)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Ocean Engineering, 1984.
FPGA-based Accelerator for Post-Quantum Signature Scheme SPHINCS-256 (2018)

In recent years, a substantial amount of research has been conducted and progress made in the area of quantum computers. Small functional prototypes have already been reported. If they scale as expected, they will eventually be able to break current public-key cryptosystems. The goal of post-quantum cryptography is to develop cryptographic systems that are secure against attacks originating from both quantum and classical computers. Frequently referred post-quantum signature schemes are based on the security of hash functions. A promising candidate in this group is SPHINCS-256. This paper presents the first FPGA-based hardware accelerator for SPHINCS-256. It can be implemented on an entry-level FPGA, occupying roughly 19,000 LUTs, 38,000 FFs and 36 BRAMs. On a Kintex-7 Xilinx FPGA, signing takes 1.53 milliseconds, and verification needs only 65 microseconds. Area and throughput of the accelerator are in a range that outperform today’s widely used RSA signature scheme. The performance can even keep up with ECDSA accelerators. Hence, SPHINCS-256 is a hot candidate to replace RSA and ECDSA in a post-quantum world.
Laboratory and field measurements and evaluations of vibration at the handles of riveting hammers (2012)

The use of riveting hammers can expose workers to harmful levels of hand-transmitted vibration (HTV). As a part of efforts to reduce HTV exposures through tool selection, the primary objective of this study was to evaluate the applicability of a standardized laboratory-based riveting hammer assessment protocol for screening riveting hammers. The second objective was to characterize the vibration emissions of reduced vibration riveting hammers and to make approximations of the HTV exposures of workers operating these tools in actual work tasks. Eight pneumatic riveting hammers were selected for the study. They were first assessed in a laboratory using the standardized method for measuring vibration emissions at the tool handle. The tools were then further assessed under actual working conditions during three aircraft sheet metal riveting tasks. Although the average vibration magnitudes of the riveting hammers measured in the laboratory test were considerably different from those measured in the field study, the rank orders of the tools determined via these tests were fairly consistent, especially for the lower vibration tools. This study identified four tools that consistently exhibited lower frequency-weighted and unweighted accelerations in both the laboratory and workplace evaluations. These observations suggest that the standardized riveting hammer test is acceptable for identifying tools that could be expected to exhibit lower vibrations in workplace environments. However, the large differences between the accelerations measured in the laboratory and field suggest that the standardized laboratory-based tool assessment is not suitable for estimating workplace riveting hammer HTV exposures. Based on the frequency-weighted accelerations measured at the tool handles during the three work tasks, the sheet metal mechanics assigned to these tasks at the studied workplace are unlikely to exceed the daily vibration exposure action value (2.5 m s(-2)) using any of the evaluated riveting hammers.
Moonlighting in Rickettsiales: Expanding Virulence Landscape (2022)

The order Rickettsiales includes species that cause a range of human diseases such as human granulocytic anaplasmosis (<i>Anaplasma phagocytophilum</i>), human monocytic ehrlichiosis (<i>Ehrlichia chaffeensis</i>), scrub typhus (<i>Orientia tsutsugamushi</i>), epidemic typhus (<i>Rickettsia prowazekii</i>), murine typhus (<i>R. typhi</i>), Mediterranean spotted fever (<i>R. conorii</i>), or Rocky Mountain spotted fever (<i>R. rickettsii</i>). These diseases are gaining a new momentum given their resurgence patterns and geographical expansion due to the overall rise in temperature and other human-induced pressure, thereby remaining a major public health concern. As obligate intracellular bacteria, Rickettsiales are characterized by their small genome sizes due to reductive evolution. Many pathogens employ moonlighting/multitasking proteins as virulence factors to interfere with multiple cellular processes, in different compartments, at different times during infection, augmenting their virulence. The utilization of this multitasking phenomenon by Rickettsiales as a strategy to maximize the use of their reduced protein repertoire is an emerging theme. Here, we provide an overview of the role of various moonlighting proteins in the pathogenicity of these species. Despite the challenges that lie ahead to determine the multiple potential faces of every single protein in Rickettsiales, the available examples anticipate this multifunctionality as an essential and intrinsic feature of these obligates and should be integrated into available moonlighting repositories.
Segmentations of MRI images of the female pelvic floor: A study of inter‐ and intra‐reader reliability (2011)

Undirected manual segmentation of the pelvic floor organs are adequate for locating the organs, but poor at defining structural boundaries.
A Scalable Multicast Hybrid Broadband Crossbar Wavelength Selective Switch For Datacenters (2021)

We present a new switching architecture that is wavelength selective and can multicast. We compare the switch loss, number of elements and crosstalk with multi-wavelength selective crossbar switch. We report reduction in number of elements of 50%, reduced loss and a similar crosstalk as compared with multi-wavelength selective crossbar switch.
Valsartan restores inflammatory response by macrophages in adipose and hepatic tissues of LPS-infused mice (2012)

Inflammation involving adipose tissue is regarded as one of the major molecular mechanisms underlying obesity-related insulin resistance. Recent studies have suggested a series of angiotensin II receptor blockers (ARBs) to improve insulin resistance or protect against the development of diabetes mellitus. We previously demonstrated that valsartan suppresses the inflammatory response of macrophages. Interestingly, however, this effect did not occur via peroxisome proliferator-activated receptor (PPAR) γ or the AT1a receptor. This suppression appears to secondarily lead to amelioration of insulin resistance and reductions in abnormal gene expressions in adipocytes. In addition to these in vitro findings, we herein demonstrate the in vivo effects of valsartan, using mice constitutively infused with lipopolysaccharide (LPS) for 4 weeks. Oral administration of valsartan to LPS-infused mice normalized the increased expressions of inflammatory cytokines in adipose and liver tissues. These results raise the possibility that valsartan not only contributes to normalization of obesity-related insulin resistance, but is also beneficial for the treatment of other diseases with inflammation related to the metabolic syndrome such as atherosclerosis and non-alcoholic steatohepatitis. Further study is necessary to clarify these issues.
Single Cell Analysis of RNA-mediated Histone H3.3 Recruitment to a Cytomegalovirus Promoter-regulated Transcription Site (2013)

Unlike the core histones, which are incorporated into nucleosomes concomitant with DNA replication, histone H3.3 is synthesized throughout the cell cycle and utilized for replication-independent (RI) chromatin assembly. The RI incorporation of H3.3 into nucleosomes is highly conserved and occurs at both euchromatin and heterochromatin. However, neither the mechanism of H3.3 recruitment nor its essential function is well understood. Several different chaperones regulate H3.3 assembly at distinct sites. The H3.3 chaperone, Daxx, and the chromatin-remodeling factor, ATRX, are required for H3.3 incorporation and heterochromatic silencing at telomeres, pericentromeres, and the cytomegalovirus (CMV) promoter. By evaluating H3.3 dynamics at a CMV promoter-regulated transcription site in a genetic background in which RI chromatin assembly is blocked, we have been able to decipher the regulatory events upstream of RI nucleosomal deposition. We find that at the activated transcription site, H3.3 accumulates with sense and antisense RNA, suggesting that it is recruited through an RNA-mediated mechanism. Sense and antisense transcription also increases after H3.3 knockdown, suggesting that the RNA signal is amplified when chromatin assembly is blocked and attenuated by nucleosomal deposition. Additionally, we find that H3.3 is still recruited after Daxx knockdown, supporting a chaperone-independent recruitment mechanism. Sequences in the H3.3 N-terminal tail and αN helix mediate both its recruitment to RNA at the activated transcription site and its interaction with double-stranded RNA in vitro. Interestingly, the H3.3 gain-of-function pediatric glioblastoma mutations, G34R and K27M, differentially affect H3.3 affinity in these assays, suggesting that disruption of an RNA-mediated regulatory event could drive malignant transformation.