gebhart/patrepeval huggingface dataset:
Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations (2019)

Abstract Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~30×) of five native trios from Malaysia, and discovered approximately 6.9 million single nucleotide variants (SNVs), 1.2 million small insertions and deletions (indels), and 9,000 copy number variants (CNVs) in the 15 samples. We found 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify autosomal de novo variants and estimated the mutation rates to be 0.81×10-8–1.33×10-8 , 1.0×10-9–2.9×10-9, and ~0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for accurate haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example was a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.
Three-dimensional Thermal Analysis of a Waveguide Ge/Si Photodiode (2010)

The spatial temperature distribution of a high power Ge/Si waveguide n-i-p photodiode is experimentally obtained using a time-domain thermoreflectance imaging technique. Measurement results are shown to be in good agreement with simulated values.
Reconstructing Dense Light Field From Array of Multifocus Images for Novel View Synthesis (2006)

This paper presents a novel method for synthesizing a novel view from two sets of differently focused images taken by an aperture camera array for a scene consisting of two approximately constant depths. The proposed method consists of two steps. The first step is a view interpolation to reconstruct an all-in-focus dense light field of the scene. The second step is to synthesize a novel view by a light-field rendering technique from the reconstructed dense light field. The view interpolation in the first step can be achieved simply by linear filters that are designed to shift different object regions separately, without region segmentation. The proposed method can effectively create a dense array of pin-hole cameras (i.e., all-in-focus images), so that the novel view can be synthesized with better quality.
2-(2,3,5,6-Tetrafluoro-4-iodoanilino)ethanol (2007)

The reaction of 2-amino-ethanol and iodo-penta-fluoro-benzene in the presence of K(2)CO(3) gave the title compound, C(8)H(6)F(4)INO, in high yield. The structure is characterized by double layers of mol-ecules linked by O-H⋯O and N-H⋯O hydrogen bonds, and linear C-I⋯F [I⋯F = 3.049 (2) Å] and bent C-I⋯I [I⋯I = 3.9388 (7) Å] inter-actions between pairs of nearly parallel iodo-tetra-fluoro-phenyl groups. No O⋯I or N⋯I halogen bonding is found.
Tailored Patient Information: Some Issues and Questions (1997)

Tailored patient information (TPI) systems are computer programs which produce personalised heath-information material for patients. TPI systems are of growing interest to the natural-language generation (NLG) community; many TPI systems have also been developed in the medical community, usually with mail-merge technology. No matter what technology is used, experience shows that it is not easy to field a TPI system, even if it is shown to be effective in clinical trials. In this paper we discuss some of the difficulties in fielding TPI systems. This is based on our experiences with 2 TPI systems, one for generating asthma-information booklets and one for generating smoking-cessation letters.
A Gradiometric Magnetic Sensor System for Stray-Field-Immune Rotary Position Sensing in Harsh Environment (2018)

Contactless magnetic position sensors are used in countless industrial and automotive applications. However, as a consequence of the electrification trend the sensors can be exposed to parasitic magnetic stray fields, and their desired robustness may be compromised. In this paper we publish for the first time how this challenge is addressed and constructively solved using a complete paradigm change leaving conventional magnetic field measurement behind and entering into the realm of magnetic field gradient measurement. Our novel sensor system consists of an integrated Hall sensor realized in 0.18 &mu;m CMOS technology with magnetic concentrators and a four-pole permanent magnet. The intrinsic angular accuracy was assessed comparing the rotary position of the permanent magnet with the sensor output showing angle errors below 0.3&deg;. Additional end-of-line calibration can be applied using built-in memory and processing capability to further increase the accuracy. Finally, we demonstrate the immunity against stray fields of 4000 A/m which led to errors below 0.1&deg;, corresponding to 0.06% of the sensors fullscale angular range. In conclusion, this novel sensor system offers a compact and flexible solution for stray-field immune rotary position measurement in harsh environment.
Abnormal Fhit expression in malignant and premalignant lesions of the cervix. (1999)

Genetic analysis of cervical cancer has demonstrated frequent allelic loss in the 3p chromosomal region. The newly described gene FHIT is located at chromosome region 3p14.2, and its expression has been demonstrated previously by reverse transcription-PCR to be abnormal in a majority of cervical cancer cell lines. In this study, 98 different lesions of the cervix were examined for Fhit expression by immunohistochemical staining. Whereas normal cervical epithelium demonstrated diffuse, moderate to intense cytoplasmic staining, many pathological lesions of the cervix displayed reduced or absent Fhit expression. Sixty-one percent of squamous carcinomas and 40% of adenocarcinomas of the cervix had abnormal Fhit expression. Sixty-five preneoplastic lesions of the cervix were examined. Eleven of 33 high-grade squamous intraepithelial lesions and 1 of 12 low-grade squamous intraepithelial lesions had abnormal Fhit expression. In summary, Fhit expression is frequently abnormal in both glandular and squamous cervical cancers, with a higher frequency of Fhit alterations observed in squamous lesions. In addition, abnormal Fhit expression can be detected in some preneoplastic lesions of the ectocervix. Alterations in Fhit expression may be an important marker of early progression in the development of cancers of the cervix.
Synapse-specific diversity of distinct postsynaptic GluN2 subtypes defines transmission strength in spinal lamina I (2023)

ABSTRACT The unitary postsynaptic response to presynaptic quantal glutamate release is the fundamental basis of excitatory information transfer between neurons. The view, however, of individual glutamatergic synaptic connections in a population as homogenous, fixed-strength units of neural communication is becoming increasingly scrutinized. Here, we used minimal stimulation of individual glutamatergic afferent axons to evoke single synapse resolution postsynaptic responses from central sensory lamina I neurons in an ex vivo adult rat spinal slice preparation. We detected unitary events exhibiting a NMDA receptor component with distinct kinetic properties across synapses conferred by specific GluN2 subunit composition, indicative of GluN2 subtype-based postsynaptic heterogeneity. GluN2A, 2A and 2B, or 2B and 2D synaptic predominance functioned on distinct lamina I neuron types to narrowly, intermediately, or widely tune, respectively, the duration of evoked unitary depolarization events from resting membrane potential, which enabled individual synapses to grade differentially depolarizing steps during temporally-patterned afferent input. Our results lead to a model wherein a core locus of proteomic complexity prevails at this central glutamatergic sensory synapse that involves distinct GluN2 subtype configurations. These findings have major implications for subthreshold integrative capacity and transmission strength in spinal lamina I and other CNS regions.
Abstract 6585: Systems biology for investigating drug resistance mechanism of melanoma (2020)

Abstract Integrated proteomic and metabolic single-cell assays reveal multiple independent adaptive responses to drug tolerance in a BRAF-mutant melanoma cell line Cancers commonly develop resistance against chemotherapeutics or targeted therapies through various types of genetic or non-genetic mechanisms. Non-genetic mechanisms have been shown to occur early on and can provide a latent reservoir of cells for the emergence of various different type of mechanisms, yet very limited understanding of process were resolve main from bulk analysis. Considering the heterogeneous nature of the tumor cells, a single-cell level characterization of the process worth detailed further investigation. Using MAPK inhibition of BRAF-mutant melanomas as a model system, we resolved that cells take different paths to go from drug-sensitive to drug-resistant state. Using a microfludic-based single-cell integrated proteomic and metabolic assay, we assayed for a panel of signaling, phenotypic, and metabolic regulators at four time points during the first five days of drug treatment. Dimensional reduction of the resultant data set, coupled with information theoretic analysis, uncovered a complex cell state landscape and identified two distinct paths connecting drug-naïve and drug-tolerant states. Cells are shown to exclusively traverse one of the two pathways depending on the level of the lineage restricted transcription factor MITF in the drug-naïve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities, and are independently druggable. Our results update the paradigm of adaptive resistance development in an isogenic cell population and offer insight into the design of more effective combination therapies. Citation Format: Yapeng Su, Guideng Li, Melissa Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Lidia Robert, Raphael Levine, Antoni Ribas, Garry Nolan, Wei Wei, Sylvia Plevritis, David Baltimore, James R. Heath. Systems biology for investigating drug resistance mechanism of melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6585.
Growth hormone receptor gene disruption in mature‐adult mice improves male insulin sensitivity and extends female lifespan (2021)

Studies in multiple species indicate that reducing growth hormone (GH) action enhances healthy lifespan. In fact, GH receptor knockout (GHRKO) mice hold the Methuselah prize for the world's longest-lived laboratory mouse. We previously demonstrated that GHR ablation starting at puberty (1.5 months), improved insulin sensitivity and female lifespan but results in markedly reduced body size. In this study, we investigated the effects of GHR disruption in mature-adult mice at 6 months old (6mGHRKO). These mice exhibited GH resistance (reduced IGF-1 and elevated GH serum levels), increased body adiposity, reduced lean mass, and minimal effects on body length. Importantly, 6mGHRKO males have enhanced insulin sensitivity and reduced neoplasms while females exhibited increased median and maximal lifespan. Furthermore, fasting glucose and oxidative damage was reduced in females compared to males irrespective of Ghr deletion. Overall, disrupted GH action in adult mice resulted in sexual dimorphic effects suggesting that GH reduction at older ages may have gerotherapeutic effects.
The Role of Uncompensated Spins in Exchange Biasing (2006)

A unidirectional horizontal shift of the magnetic hysteresis loop, the exchange bias effect (EB-effect) is observed when the system is field cooled below the Neel temperature of the antiferromagnet AFM. It is widely accepted that pinned, and uncompensated spins of the AFM are responsible for the exchange bias effect. Here we analyse MFM and magnetometry data obtained on two different exchange biased AFM/FM systems. Both samples contain Co/Pt multilayers as ferromagnetic layers.
An Endonuclease Induced after Infection of Escherichia coli with Bacteriophage T7 (1970)

Abstract A deoxyribonuclease has been purified 1,800-fold from Escherichia coli infected with bacteriophage T7. The enzyme has an approximate molecular weight of 18,000, requires a divalent cation for activity, and is inhibited by high concentrations of RNA. The purified enzyme catalyzes an endonucleolytic cleavage of both single- and double-stranded DNA. The rate of hydrolysis of single-stranded DNA is 150-fold that of double-stranded DNA. The hydrolysis of single-stranded DNA results in the formation of acid-soluble oligonucleotides. No acid-soluble products have been observed during the hydrolysis of double-stranded DNA. Identity of the activities toward single- and double-stranded DNA is supported by identical sedimentation rates in sucrose gradients, reaction requirements, rates of heat inactivation, and genetic analysis.
Development of Pneumatic Master-Slave Hand and Joint Control (2008)

Recently, research and development has focused on robots that work in place of people. It is necessary for robots to perform the same flexible motions as people. Additionally, such robots need to incorporate high-level safety features in order not to injure people. For realization of such robots, we need to develop a robot hand that functions like a human hand. At the same time, this type of robot hand can be used as an artificial hand. Here, we present artificial muscle-type pneumatic actuators as the driving source of a robot hand that is both safe and flexible. Some development of robot hands using pneumatic actuators has already taken place. But, until now, when a pneumatic actuator is used, a big compressor is needed. So, the driving system also needs to be big; enlargement of the driving system is a major problem. Consequently, in this research, we develop a low-pressure, low-volume pneumatic actuator for driving a robot hand that works flexibly and safely on the assumption that it will be in contact with people. We develop a five-fingered robot hand with pneumatic actuators. And, we construct a master-slave system to enable the robot hand to perform the same operations as a human hand. We make a 1-link arm that has one degree of freedom using a pneumatic actuator, and construct a control system for the 1-link arm and verify its control performance.
A Novel Bio-Microelectromechanical System for In Vivo Diagnostic Monitoring of Fracture Healing (2013)

The ability to detect a normal from aberrant bone healing cascade during the acute fracture fixation period (1–3 weeks post trauma) is critically important to insure a favorable clinical outcome for many complex fracture cases. Radiographic evaluations do not have the inherent fidelity to make qualitative predictions during the acute healing phase. Early detection of an atypical healing profile would allow for revision strategies to be employed without the need for expensive and undesirable follow-up surgeries. In an effort to address the critical need to diagnose the course of bone fracture healing in the vitally important early healing phase, our research group has developed a radio frequency (RF) strain sensor that takes advantages of the recent advances in meta-materials and micro-electo-mechanical systems (MEMS) technology. Our MEMS sensor is biocompatible (bioMEMS), inductively powered and monitors the surface strains on implanted hardware [1, 2]. Another novel feature of this new sensor is that it does not require an internal-external physical connection to sense and transmit in vivo biological data. The essence of the sensor’s design is that straining the integrated RF bioMEMS circuit results in a shift in its resonant frequency (ResF). Through telemetric detection of this ResF shift, it is possible to longitudinally monitor the temporal changes in hardware strain. It is well understood that that as proper fracture healing progresses (i.e. increasingly stable tissue(s) stabilizing the fracture sight) that the load/strain born by orthopaedic implant diminishes. Therefore, telemetric measurements of our bioMEMS system (i.e. hardware load/strain) provide direct insight into the degree of fracture stabilization and healing.
Analyzing the input stream for character- level errors in unconstrained text entry evaluations (2006)

Recent improvements in text entry error rate measurement have enabled the running of text entry experiments in which subjects are free to correct errors (or not) as they transcribe a presented string. In these “unconstrained” experiments, it is no longer necessary to force subjects to unnaturally maintain synchronicity with presented text for the sake of performing overall error rate calculations. However, the calculation of character-level error rates, which can be trivial in artificially constrained evaluations, is far more complicated in unconstrained text entry evaluations because it is difficult to infer a subject's intention at every character. For this reason, prior character-level error analyses for unconstrained experiments have only compared presented and transcribed strings, not input streams. But input streams are rich sources of character-level error information, since they contain all of the text entered (and erased) by a subject. The current work presents an algorithm for the automated analysis of character-level errors in input streams for unconstrained text entry evaluations. It also presents new character-level metrics that can aid method designers in refining text entry methods. To exercise these metrics, we perform two analyses on data from an actual text entry experiment. One analysis, available from the prior work, uses only presented and transcribed strings. The other analysis uses input streams, as described in the current work. The results confirm that input stream error analysis yields richer information for the same empirical data. To facilitate the use of these new analyses, we offer pseudocode and downloadable software for performing unconstrained text entry experiments and analyzing data.
Discovery and Kinetic Profiling of 7-Aryl-1,2,4-triazolo[4,3-a]pyridines: Positive Allosteric Modulators of the Metabotropic Glutamate Receptor 2 (2017)

We report the synthesis and biological evaluation of a series of 7-aryl-1,2,4-triazolo[4,3-a]pyridines with mGlu<sub>2</sub> positive allosteric modulator (PAM) activity and affinity. Besides traditional in vitro parameters of potency and affinity, kinetic parameters k<sub>on</sub>, k<sub>off</sub> and residence time (RT) were determined. The PAMs showed various kinetic profiles; k<sub>on</sub> values ranged over 2 orders of magnitude, whereas RT values were within a 10-fold range. Association rate constant k<sub>on</sub> was linearly correlated to affinity. Evaluation of a short, medium, and long RT compound in a label-free assay indicated a correlation between RT and functional effect. The effects of long RT compound 9 on sleep-wake states indicated long RT was translated into sustained inhibition of rapid eye movement (REM) in vivo. These results show that affinity-only driven selection would have resulted in mGlu<sub>2</sub> PAMs with high values for k<sub>on</sub> but not necessarily optimized RT, which is key to predicting optimal efficacy in vivo.
Invasive Fungal Infections among Organ Transplant Recipients: Results of the Transplant‐Associated Infection Surveillance Network (TRANSNET) (2010)

We detected a slight increase in IFIs during the surveillance period. These data provide important insights into the timing and incidence of IFIs among organ transplant recipients, which can help to focus effective prevention and treatment strategies.
Inter‐ and intra‐instar food consumption in the German cockroach, Blattella germanica (1996)

Abstract Food consumption was measured in an insecticide‐susceptible (Orlando) and ‐resistant (Village Green) strain of German cockroach, Blattella germanica (Dictyoptera: Blattellidae), throughout each stadium. All instars exhibited a similar pattern of consumption over the course of the instar; consumption was low to moderate at the beginning of each instar, climbed steadily to a maximum near the middle, declined progressively from the mid‐instar maximum, and ceased or was minimal several days before the next molt. Consumption ceased or was minimal during the final two to four days of each instar. Cumulative consumption for the six instars was significantly greater in the Village Green strain as compared with the Orlando strain. Village Green nymphs consumed 79.6 ± 0.7 mg of rat chow while Orlando nymphs consumed 63.7 ± 3.4 mg. Total consumption by instar increased significantly with each successive instar in the Village Green strain. In addition, Village Green sixth instar females consumed significantly more food than sixth instar males. A similar trend was observed for the Orlando strain; consumption tended to increase in each successive instar. Relative consumption rate (food consumed/cockroach/instar divided by the mean weight of the instar) was highest in the first two instars and decreased in subsequent instars.
Sliceable bandwidth variable transponder: The IDEALIST vision (2015)

This paper reports on the general architecture for a sliceable bandwidth variable transponder as discussed within the IDEALIST European project. Support for super-channels (optical connections with several adjacent sub-carriers) and slice-ability (super-channels generated together but independently routed in the network towards different destinations) is guaranteed. For illustrative purpose some driving ideas on a possible modular implementation are shown.
Band-Limited Digital Predistortion with Band-Switching Feedback Architecture for 5G mmWave Power Amplifiers (2018)

This paper presents a novel band-limited digital predistortion (BL-DPD) with band-switching feedback architecture and update procedure for linearization of a wideband 5G mmWave power amplifier (PA). In the proposed BL-DPD, inside and outside of original input signal band in PA output are acquired alternately. This is done while keeping ADC bandwidth same as original input signal bandwidth, thus, avoiding increase in cost and energy consumption. It is demonstrated that the proposed BL-DPD achieves ACLR of -43.6/-42 dBc and EVM <; 3% for Watt-class PA operating on a 256 QAM modulated 26 GHz OFDM signal with bandwidth of 800 MHz.
ChemInform Abstract: Enzymatic Resolution of α,α‐Disubstituted α‐Amino Acid Esters and Amides. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.