gebhart/patrepeval huggingface dataset:
Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay (2022)

Copy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10<sup>-4</sup>), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.
Constructing “Designer Atoms” via Resonant Graphene-Induced Lamb Shifts (2017)

The properties of an electron in an atom or molecule are not fixed; rather they are a function of the optical environment of the emitter. Not only is the spontaneous emission a function of the optical environment, but also the underlying wave functions and energy levels, which are modified by the potential induced by quantum fluctuations of the electromagnetic field. In free space, this modification of atomic levels and wave functions is very weak and generally hard to observe due to the prevalence of other perturbations like fine structure. Here, we explore the possibility of highly tailorable electronic structure by exploiting large Lamb shifts in tunable electromagnetic environments such as graphene, whose optical properties are dynamically controlled via doping. The Fermi energy can be chosen so that the Lamb shift is very weak, but it can also be chosen so that the shifts become more prominent than the fine structure of the atom and even potentially the Coulomb interaction with the nucleus. Potential implications of this idea include being able to electronically shift an unfavorable emitter structure into a favorable one, a new approach to probe near-field physics in fluorescence, and a way to access regimes of physics where vacuum fluctuations are not a weak perturbation but rather the dominant physics.
Downregulation of miR-15a and miR-16-1 at 13q14 in Chronic Lymphocytic Leukemia (2016)

Featured Article: Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2002;99:15524–9.2

MicroRNAs (miRNAs)3 are involved in many biological processes due to their posttranscriptional gene regulation function. Consequently, their crucial role in many diseases, including cancer, is now well known. Nevertheless, the connection between miRNA deregulation and tumorigenesis was unclear for quite some time. In the 2002 article discussed here (1), Dr. Croce's group reported the very first direct association between miRNAs and cancer. In the time preceding this important discovery, Dr. Croce devoted himself to the study of the most common human leukemia: chronic lymphocytic leukemia (CLL). CLL is a malignancy of CD5-positive B cells occurring, for the most part, in individuals over the age of 60 years. At presentation the disease is usually indolent, although it often progresses to an aggressive form. An aggressive form at presentation occurs in 30% of patients. Consistent chromosomal …
Electron Density Guided Fragment-Based Lead Discovery of Ketohexokinase Inhibitors (2010)

A fragment-based drug design paradigm has been successfully applied in the discovery of lead series of ketohexokinase inhibitors. The paradigm consists of three iterations of design, synthesis, and X-ray crystallographic screening to progress low molecular weight fragments to leadlike compounds. Applying electron density of fragments within the protein binding site as defined by X-ray crystallography, one can generate target specific leads without the use of affinity data. Our approach contrasts with most fragment-based drug design methodology where solution activity is a main design guide. Herein we describe the discovery of submicromolar ketohexokinase inhibitors with promising druglike properties.
State-Dependent Relay Channel: Achievable Rate and Capacity of a Semideterministic Class (2013)

This paper considers the problem of communicating over a relay channel with state when noncausal state information is partially available at the nodes. We first establish a lower bound on the achievable rates based on noisy network coding and Gelfand-Pinsker coding, and show that it provides an alternative characterization of a previously known bound. We then introduce the class of state-decoupled relay channels and show that our lower bound is tight for a subclass of semideterministic channels. We also compute the capacity for two specific examples of this subclass - a channel with multiplicative binary fading and a channel with additive Gaussian interference. These examples are not special cases of previous classes of semideterministic relay channels with known capacity.
Abstract 2903: A novel compound induces synthetic lethality for p53 mutations in osteosarcoma cells (2018)

Abstract Osteosarcoma is the second-highest cause of cancer-related death in children and adolescents. Despite advances in chemotherapy and surgery, the survival rate for metastatic osteosarcoma remains below 30% for the last three decades. Discovery of new chemotherapy agents would be crucial for improving outcomes of osteosarcoma patients. Here, using high-throughput screening, we have found a new compound, called 2-{2-[(3,5-dimethoxybenzyl)sulfanyl]-1,3-thiazol-4-yl}-N-(2-thienylmethyl)acetamide (referred to as KU0171032), as an inducer of apoptosis in various canine and human osteosarcoma cells. This compound shows minimal effects on non-transformed osteoblast and fibroblast cells. Intriguingly, KU0171032-induced apoptosis is more robust in osteosarcoma cells having mutant p53 or null for p53, as compared to cells with wild-type p53. Knockdown of wild-type p53 in U2OS and SJSA-1 cells significantly enhances sensitivity to KU0171032 with increase in DNA damage and caspase-3 cleavage. Moreover, KU0171032 significantly reduces in vivo tumor growth of osteosarcoma cells with p53 knockdown or carrying mutant p53. Our results strongly suggest that KU0171032 shows synthetic lethality with p53 mutations in osteosarcoma cells. Given that loss of p53 activity is frequent event in many cancer types including osteosarcoma while normal cells usually retain wild-type p53, this compound could be used to develop novel therapeutic strategies that capitalize on vulnerabilities in osteosarcoma and other types of cancer. Citation Format: Tomoo Iwakuma, Alejandro Parrales, Peter McDonald, Anuradha Roy, Mitchell W. Braun, Frank J. Schoenen, Jenna Wang, Steve Rogers, Melinda Broward, Tyce Bruns, Shrikant Anant, Dan A. Dixon, Fred Meyer, Katherine M. Chastain, Douglas H. Thamm, Scott J. Weir, Kathleen Neville, Joy M. Fulbright. A novel compound induces synthetic lethality for p53 mutations in osteosarcoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2903.
Distributed Speech Recognition (2012)

This chapter contains sections titled: Elements of distributed speech processing Front-end processing ETSI standards Transfer protocol Energy-aware distributed speech recognition ESR, NSR, DSR Bibliography
Gender-related differences in MEN1 lesion occurrence and diagnosis: a cohort study of 734 cases from the Groupe d'étude des Tumeurs Endocrines (2011)

The phenotype expression of the MEN1 disease gene was different in males and females. In female patients, the possibility of MEN1 is not sufficiently taken into account. Any patient presenting a lesion that belongs to the MEN1 spectrum, such as a pituitary tumor, should be closely questioned about their family history and should be tested for hypercalcemia.
The Induction of Nitric Oxide by Interleukin-12 and Tumor Necrosis Factor- in Human Natural Killer Cells: Relationship With the Regulation of Lytic Activity (1998)

We have investigated the interleukin-12 (IL-12) and tumor necrosis factor- (TNF)-induced regulation of human natural killer (NK) cell function and their relationship with nitric oxide (NO) generation. We demonstrate that both cytokines were efficient to trigger the transcription of the inducible nitric oxide synthase (iNOS) mRNA, as detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Western blot analysis and intracytoplasmic fluorescence showed that iNOS protein was also induced by both cytokines. However, our data indicate that NO does not play a significant role in the effector phase of the cytotoxic activity mediated by NK-stimulated cells, inasmuch as the lytic activity was not affected in the presence of specific NO synthase inhibitors. When aminoguanidine (AMG), an inhibitor of iNOS, was added during the afferent phase of NK stimulation with IL-12 and TNF, a subsequent increase in the lytic potential of the effector cells towards the NK-sensitive target cells (K562) and lymphokine-activated killer (LAK) target cells (Daudi) was observed. Conversely, the addition of chemical NO donors during the afferent step resulted in a dose-dependent inhibition of the NK and LAK cytotoxicity. Our data suggest that the enhancement of NK-cell cytotoxic activity resulting from iNOS inhibition may be correlated, at least in part, to an increase in interferon-γ production and granzyme B expression. © 1998 by The American Society of Hematology.
Distributed Acoustic Sensing measurement by using seafloor optical fiber cable system off Sanriku for seismic observation (2019)

Recently Distributed Acoustic Sensing (DAS) measurement which utilizes an optical fiber itself as a sensor becomes popular. In 1996, a seafloor seismic tsunami observation system using an optical fiber cable was deployed off Sanriku by Earthquake Research Institute, the University of Tokyo. The system has spare (dark) optical fibers without repeaters. We start development of a seafloor seismic observation system by the DAS technology with Sanriku cable observation system as a next generation of marine seismic observation system. In February 2019, we made a pilot observation of a DAS measurement using a dark fiber of Sanriku seafloor observation system. The data were collected continuously for about 46 hours and many earthquakes including micro-earthquakes and a deep earthquake were recorded.
Thinking Too Classically (2019)

Quantum computing is a fundamentally different way of performing computation than classical computing. Many problems that are considered hard for classical computers may have efficient solutions using quantum computers. Recently, technology companies including IBM, Microsoft, and Google have invested in developing both quantum computing hardware and software to explore the potential of quantum computing. Because of the radical shift in computing paradigms that quantum represents, we see an opportunity to study the unique needs people have when interacting with quantum systems, what we call Quantum HCI (QHCI). Based on interviews with experts in quantum computing, we identify four areas in which HCI researchers can contribute to the field of quantum computing. These areas include understanding current and future quantum users, tools for programming and debugging quantum algorithms, visualizations of quantum states, and educational materials to train the first generation of "quantum native" programmers.
Soybean Oil and Nonthermal Plasma Pretreatment to Dye Para‐Aramid Woven Fabrics with Disperse Dye Using a Glycerol‐Based Dye Bath (2021)

Abstract High‐performance para‐aramid fibers offer a number of uses as strong, lightweight materials for protective vests, helmets, tires, and other applications. The chemically inert nature of the fibers makes them difficult to dye or durably print by conventional dyeing techniques for textiles, and solution dyeing during production of the fibers can limit the color of para‐aramid fabrics to the color of the spun yarn prior to weaving or knitting and thereby limit the practical applications of these textiles as protective outerwear. This study presents a new method developed to improve the dyeing of woven para‐aramid fabrics with a disperse dye. Specifically, sequential experimentation proves the beneficial effects of first soaking para‐aramid fabrics in soybean oil followed by surface treatment with atmospheric nonthermal plasma and using glycerol as the dispersant and sodium chloride as an electrolyte without the addition of other auxiliary chemicals. Under the optimized treatment conditions of this study, the color strength (K/S value) of dyed para‐aramid fabrics increased to 3.89 from 0.35 of the untreated samples as determined from spectral analysis of the sample reflectance in the visible range. Fourier transform infrared spectroscopy analysis revealed that the high content of unsaturated fatty acids in soybean oil and their interaction with reactive species in the ambient nonthermal plasma were the primary factors for improving the color strength of the dyed para‐aramid fabrics.
Brain Correlates of Stuttering and Syllable Production (2004)

This article reports a gender replication study of the P. T. Fox et al. (2000) performance correlation analysis of neural systems that distinguish between normal and stuttered speech in adult males. Positron-emission tomographic (PET) images of cerebral blood flow (CBF) were correlated with speech behavior scores obtained during PET imaging for 10 dextral female stuttering speakers and 10 dextral, age- and sex-matched normally fluent controls. Gender comparisons were made between the total number of voxels per region significantly correlated with speech performance (as in P. T. Fox et al., 2000) plus total voxels per region that were significantly correlated with stutter rate and not with syllable rate. Stutter-rate regional correlates were generally right-sided in males, but bilateral in the females. For both sexes the positive regional correlates for stuttering were in right (R) anterior insula and the negative correlates were in R Brodmann area 21/22 and an area within left (L) inferior frontal gyrus. ...
Data from Fine-tuning Tumor Immunity with Integrin Trans-regulation (2023)

&lt;div&gt;Abstract&lt;p&gt;Inefficient T-cell homing to tissues limits adoptive T-cell immunotherapy of solid tumors. αLβ2 and α4β1 integrins mediate trafficking of T cells into tissues via engagement of ICAM-1 and VCAM-1, respectively. Inhibiting protein kinase A (PKA)–mediated phosphorylation of α4 integrin in cells results in an increase in αLβ2-mediated migration on mixed ICAM-1–VCAM-1 substrates &lt;i&gt;in vitro&lt;/i&gt;, a phenomenon termed “integrin trans-regulation.” Here, we created an α4(S988A)-bearing mouse, which precludes PKA-mediated α4 phosphorylation, to examine the effect of integrin trans-regulation &lt;i&gt;in vivo&lt;/i&gt;. The α4(S988A) mouse exhibited a dramatic and selective increase in migration of lymphocytes, but not myeloid cells, to sites of inflammation. Importantly, we found that the α4(S988A) mice exhibited a marked increase in T-cell entry into and reduced growth of B16 melanomas, consistent with antitumor roles of infiltrating T cells and progrowth functions of tumor-associated macrophages. Thus, increased α4 trans-regulation of αLβ2 integrin function biases leukocyte emigration toward lymphocytes relative to myeloid cells and enhances tumor immunity. &lt;i&gt;Cancer Immunol Res; 3(6); 661–7. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A mechanistic study of molecular sieving inorganic membranes for gas separations. Final report, [August 1, 1992--July 31, 1993] (1993)

The permeability of gases with kinetic diameters of 2.89 {Angstrom} to 3.9 {Angstrom} were measured through microporous silica hollow fiber membranes at 298 K to 473 K at 20 atm feed gas pressure. Permeabilities ranged from 0.01 Barrer to 1000 Barrer and were inversely proportional to the kinetic diameter of the penetrant. Linear Arrhenius plots were obtained from permeability data activation energies ranged from 7.5 to 13.5 kcal/mole. The activation energies for the hollow Tiber membranes were consistent with literature data for diffusion of hydrocarbons in zeolites. High separation factors were obtained for O{sub 2}/N{sub 2} and CO{sub 2}/CH{sub 2} mixtures. The mixture separation factors for O{sub 2}/N{sub 2} decreased from 11.5 at 298 K to 4.6 at 423 K. Over the same temperature range, CO{sub 2}/CH{sub 2} separation factors decreased from 186 to 22.3. Separation factors for O{sub 2}/N{sub 2} mixtures were up to 20% larger than the values obtained from pure gas measurements below 373 K. A similar effect was seen for CO{sub 2}/CH{sub 2} mixtures after the membrane had been heated to at least 398 K and then cooled in inert gas flow. Differences between separation factors and ideal gas values is attributed to a competitive adsorption effect where the more strongly interacting gases (O{sub 2}, CO{sub 2}) saturate the surface and block the transport of weakly interacting gases (N{sub 2}, CH{sub 4}).
Global Change and the Dark of the Moon (1992)

We have considered the possibility of using earthshine to measure the reflectance properties of the earth (albedo and phase function). Measurements of earthshine carried out by Danjon in 1926--33 show that even then the average albedo could be determined with a precision of +/- 0.01 and that both synoptic and seasonal variations could be observed clearly. We show that, after correction for wavelength dependence and the opposition effect in the lunar reflectance properties, Danjon's visual albedo of 0.40 can be reconciled with the ERBE satellite Bond albedo of 0.30. We recommend a modern earthshine monitoring program (advantages include global integration, continuous coverage, ground basing, and low cost) as a complement to present and planned satellite measurements.
Experimental investigation of droplet biosensing by multi-wavelength plasmonic (2012)

Surface Plasmons Resonance (SPR) architectures involving multi-wavelength interrogation is an attractive alternative for droplet biosensing. In this work, we address two detection formats experimentally investigated by our research group. The first one involves an angular scanning combining one near-IR and one visible light probes. It enables to increase the number of parameters for numerical fitting, which improves the precision of measurement. The second concept involves the SPR Coupler and Disperser sensor principle, where the spectrum analysis is performed on each detector pixel using the same diffraction grating that is employed for the optical coupling of the incident light with the surface plasmons.
Observing ultrastructural changes in Pagumogonimus skrjabini due to triclabendazole and praziquantel. (2010)

Objectives To observe the ultrastructural changes in Pagumogonimus skrjabini after subjection to triclabendazole and praziquantel.Methods Thirty SD mice were randomly divided into a triclabendazole treatment group,a praziquantel treatment group,and a control group.They were each injected through the abdominal cavity with metacercariae of P.skrjabini.Rats in the two treatment groups in which P.skrjabini was detected in the feces were treated on the 60th day after infection,and mice were dissected and the worms recovered were observed under a transmission electron microscope on the third day after treatment.Results Teguments of worms in the triclabendazole treatment group disappeared,basal plasma membranes were disrupted,and the muscular layer was necrotic.The external plasma membrane and matrix of worms in the triclabendazole treatment group disappeared,and a muscular layer was present but disorganized.Worms had complete body wall structures in the control group.Conclusion The body walls of P.skrjabini are damaged by triclabendazole and praziquantel,and triclabendazole causes more damage than praziquantel.
Smart Baroreceptor Activation Therapy Strikingly Attenuates Blood Pressure Variability in Hypertensive Rats With Impaired Baroreceptor (2019)

Increased blood pressure (BP) variability (BPV) is an independent risk factor of cardiovascular events among hypertensive patients. The arterial baroreceptor reflex is a powerful regulator of BP and attenuates BPV via a sympathetic negative feedback control. Conventional baroreceptor activation therapy (cBAT) electrically stimulates the carotid baroreceptors with constant stimulation parameters. While cBAT lowers BP, it does not mount a pressure feedback mechanism. We hypothesized that baroreceptor activation therapy with a pressure feedback system (smart BAT [sBAT]) is able to reduce BPV as well as lower BP. We developed sBAT that electrically stimulated baroreceptors at a frequency proportional to the difference between instantaneous BP and a preset reference pressure, and compared its performance with cBAT. In 14-week-old spontaneously hypertensive rats (n=6), we implanted BP telemeter and created impaired arterial baroreceptors by modified sino-aortic denervation. One week after surgical preparation, we administered sBAT, cBAT or no stimulation (sham) for 15 minutes and compared BP and BPV under freely moving condition. Both cBAT and sBAT significantly lowered mean BP (sham, 141.3±12.8; cBAT, 114.3±11.4; and sBAT, 112.0±7.3 mm Hg). Conventional BAT did not affect BPV at all, while sBAT significantly reduced BPV (sham, 15.4±2.6; cBAT, 16.0±5.2; and sBAT, 9.7±3.3 mm Hg). sBAT also prevented transient excessive BP rise and fall. In conclusion, sBAT was capable of reducing BP and attenuating BPV in hypertensive rats with impaired baroreceptor. sBAT is a novel treatment option for hypertensive patients with increased BPV.
Design of an optical interconnection network for Terabit IP router (2002)

The key to the success of next generation Internet lies in the development of Terabit IP routers. One of the challenging issues is to build a high-capacity switching system to provide high speed interconnection for a number of small-capacity router modules (RMs): where IP route lookup, packet storage, segmentation and reassembly, classification and filtering, buffer management, and packet scheduling are performed. Here, by taking advantages of optical and electronic technologies, we propose an optical interconnection network (OIN) to interconnect multiple RMs at 10Gb/s in the 1550 nm window.