gebhart/patrepeval huggingface dataset:
Fine Mapping of <i>PPH1</i> , a Gene for Familial Primary Pulmonary Hypertension, to a 3-cM Region on Chromosome 2q33 (2000)

Familial primary pulmonary hypertension (PPH) is a rare autosomal dominant disease characterized by distinctive changes in pulmonary arterioles that lead to increased pulmonary artery pressures, right ventricular failure, and death. Our previous studies had mapped the disease locus, PPH1, to a 27-cM region on chromosome 2q31-q33, with a maximum multipoint logarithm of the odds favoring genetic linkage score of 3.87 with markers D2S350 and D2S364. To narrow the minimal genetic region for PPH, we physically mapped 33 highly polymorphic microsatellite markers and used them to genotype 44 affected individuals and 133 unaffected individuals from 17 families with PPH. We observed recombination events that substantially reduced the interval for PPH1 to the approximately 3-cM region that separates D2S311 and D2S1384. This entire region lies within chromosome 2q33. A maximum two-point lod score of 7.23 at a recombination fraction of zero was obtained for marker D2S307. A maximum multipoint lod score of 7.41 was observed close to marker D2S1367. The current minimal genetic region contains multiple candidate genes for PPH, including a locus thought to play a role in lung cancer.
Graphene Oxide-Based Biocompatible 3D Mesh with a Tunable Porosity and Tensility for Cell Culture (2018)

One of the major challenges associated with modeling the influence of the cellular microenvironment on cell growth and differentiation is finding suitable substrates for growing the cells in a manner that recapitulates the cell-cell and cell-microenvironmental interactions in vitro. As one approach to address this challenge, we have developed graphene oxide (GO)-3D mesh with tunable hardness and porosity for application in cell culture systems. The synthetic method of GO-3D mesh is simple, easily reproducible, and low cost. The foundation of the method is the combination of poly(ethylene)(glycol) (PEG) and GO together with a salt-leaching approach (NaCl) in addition to a controlled application of heat during the synthetic process to tailor the mechanical properties, porosity, and pore-size distribution of the resulting GO-3D mesh. With this methodology, the hydrogel formed by PEG and GO generates a microporous mesh in the presence of the NaCl, leading to the formation of a stable 3D scaffold after extensive heating and washing. Varying the ratio of NaCl to GO controls porosity, pore size, and pore connectivity for the GO-3D mesh. When the porosity is less than 90%, with an increasing ratio of NaCl to GO, the number of pores increases with good interconnectivity. The 3D-mesh showed excellent biocompatibility with vascular cells which can take on a morphology comparable to that observed in vessels in vivo. Cell proliferation and gene expression can be determined from cells grown on the GO-3D scaffold, providing a valuable tool for investigating cell-microenvironmental changes. The GO-3D mesh described results from the synergy of the combined chemical properties of the PEG and GO with the salt-leaching methodology to generate a unique and flexible mesh that can be modified and optimized for a variety of in vitro applications.
3D Face Recognition Based on Multi-Scale Haar Transform (2013)

A 3D face recognition method based on multi-scale haar transform was proposed.The upper half face region of a 3D face model was mapped into a geometry image by mesh parameterization and linear interpolation.The geometry image was then decomposed by a multi-scale haar transform into frequency components of different scales,frequencies and orientations.The linear combination of vertical components of low frequencies was proved to be expression-invariant and was used as the facial feature.Experiments carried out in the FRGC v2.0 database achieved 98.81% Rank-1 recognition rate and 97.2% verification rate with False Accept Rate of 0.1%.
<i>Ampelomyces quisqualis</i> for Biological and Integrated Control of Powdery Mildews in Israel (1989)

Abstract An isolate of Ampelomyces quisqualis obtained from a Oidium sp. infecting Catha edulis in Israel, proved to be infective to several powdery mildew fungi belonging to the genera Oidium, Erysiphe, Sphaerotheca, Podosphaera, Uncinula , and Leveillula . In field trials, A. quisqualis parasitized the powdery mildews of cucumber, carrot and mango and reduced the disease. Hyperparasitism on Oidium mangiferae is reported for the first time. A. quisqualis was tolerant to many fungicides currently used to control powdery mildews and/or other plant diseases. In one experiment, treating powdery mildew of cucumber (cv. Hazera 205) with spores of A. quisqualis alone, significantly decreased disease severity and increased cucumber yields by approximately 50%. However, a greater increase in yield was obtained by using the fungicide pyrazophos alone or in combination with the hyperparasite. In a second experiment, using cv. Dalila, all treatments increased the yield over the untreated control which did not produce fruits. Zusammenfassung Ampelomyces quisqualis in der biologischen und integrierten Bekämpfung des Echten Mehltaus in Israel Festgestellt wurde, daß ein Ampelomyces quisqualis ‐Stimm, der aus einer Oidium sp. an Catha edulis in Israel isoliert wurde, einige der Pilze des Echten Mehltaus der Gattungen Oidium, Erysiphe, Sphaerotheca, Podosphaera, Uncinula und Leveillula parasitisieren konnte. In Feldversuchen konnte A. quisqualis Gurken‐, Möhren‐ und Mangomehltau parasitisieren und dadurch den Krankheitsbefall reduzieren. Der Hyperparasitismus an Oidium mangifera wird zum ersten Mal dokumentiert. Es wurde auch festgestellt, daß A. quisqualis gegen einige Fungizide, die ihren Einsatz als Mehltaufungizide oder auch gegen andere Krankheiten finden, unempfindlich ist. In einem Versuch wurde ermittelt, daß nach der Anwendung von A. quisqualis‐Sporen gegen Gurkenmehkau (Sorte Hazera 205) eine deutliche Reduzierung der Befallsintensität und eine Erhöhung des Gurkenertrages um 50% erzielt wurde. Jedoch wurden noch höhere Erträge erzielt, wenn entweder das Fungizid Pyrazophos alleine oder in Kombination mit dem Hyperparasit angewandt wurde. In einem zweiten Versuch mit der Sorte Dalila wurden bessere Erträge mit allen Behandlungen erzielt als in der unbehandelten Kontrolle, wo keine Gurken wuchsen.
Eradication of metastatic mouse cancers resistant to immune checkpoint blockade by suppression of myeloid-derived cells (2014)

Meeting abstracts Recent clinical trials have shown highly promising responses in a subset of patients treated with immune checkpoint inhibitory anti-programmed cell death-1, anti-programmed cell death ligand-1 (PD-1), and anti-cytotoxic T-lymphocyte-associated antigen-4 antibodies (CTLA-4) [[1][1
Utilizing the Microbiota and Machine Learning Algorithms To Assess Risk of Salmonella Contamination in Poultry Rinsate (2021)

Traditional microbiological testing methods are slow, and many molecular-based techniques rely on culture-based enrichment to overcome low limits of detection. Recent advancements in sequencing technologies may make it possible to utilize machine learning to identify patterns in microbiome data to potentially predict the presence or absence of pathogens. In this study, 299 poultry rinsate samples from various points in the processing chain were analyzed to determine if microbiota could inform about a sample's risk for containing Salmonella. Samples were culture confirmed as Salmonella positive or negative following modified U.S. Department of Agriculture Microbiological Laboratory Guidebook protocols. The culture confirmation result was used as a reference to compare with 16S sequencing data. Prechill samples tested positive (71 of 82) at a higher frequency than postchill samples (30 of 217) and contained greater microbial diversity. Due to the larger sample size, postchill samples were analyzed more thoroughly. Analysis of variance identified a significant effect of chilling on the number of genera (P < 0.001), but analysis of similarities failed to provide evidence for microbial dissimilarity between pre- and postchill samples (P = 0.001, R = 0.443). Various machine learning models were trained by using postchill samples to predict if a sample contained Salmonella on the basis of the samples' microbiota preenrichment. The optimal model was a random forest–based model with a performance as follows: accuracy (88%), sensitivity (85%), and specificity (90%). Although the algorithms described in this article are prototypes, these risk-based algorithms demonstrate the potential and need for further studies to provide insight alongside diagnostic tests. Combining risk-based information with diagnostic tools can help poultry processors make informed decisions to help identify and prevent the spread of Salmonella. These data add to the growing body of literature exploring novel ways to utilize microbiome data for predictive food safety.
Spectral Information Recovery for Compressed Image Restoration (2008)

The restoration of compressed images typically focuses on the removing of spatial artifacts caused by quantization error rather than the recovery of spectral information in compressed images. In this paper, we attempt to solve the compressed image restoration by considering the recovery of spectral information in compressed images. To this end, we convert this recovery problem to a route searching process in the high dimensional vector space spanned by all DCT coefficients. Since there are huge number of routes in the search space, we present two crucial issues in route construction: how to decide the nodes along the searching route and how to restrict the route within a reasonable sub-space. Total variation (TV) based regularization is applied to determine all the nodes in the searching process, and two constraints on the DCT coefficients are proposed to prune the searching space. Experimental results of our algorithm show a remarkable improvement in both PSNR and visual quality.
Adiponectin-mimetic novel nonapeptide rescues aberrant neuronal metabolic-associated memory deficits in Alzheimer’s disease (2021)

Our findings show that Os-pep activates AdipoR1/AMPK signaling and regulates neuronal insulin resistance and insulin signaling, which subsequently rescues memory deficits in AD and adiponectin-deficient models. Taken together, the results indicate that Os-pep, as an adiponectin-mimetic novel nonapeptide, is a valuable and promising potential therapeutic candidate to treat aberrant brain metabolism associated with AD and other neurodegenerative diseases.
Dual-Polarized, Differential Fed Microstrip Patch Antennas With Very High Interport Isolation for Full-Duplex Communication (2017)

This communication presents two dual-polarized microstrip patch antenna systems based on a single radiating element with 180° ring hybrid coupler for differential feeding to achieve high interport RF isolation. One of the implemented single-layer patch antennas provides more than 67 dB isolation between transmit (Tx) and receive (Rx) ports at 2.4 GHz while the second fabricated antenna with slot coupled Tx port along with differential feeding for Rx operation provides more than 90 dB RF isolation at 2.41 GHz between dc isolated Tx-Rx ports. Moreover, the single-layer antenna provides better than 62 dB interport isolation for 10 dB-return loss impedance bandwidth (BW) of 50 MHz. Measured interport isolation for implemented antenna with slot coupled Tx port achieves around 70 and 79 dB port to port RF isolation for 50 and 20 MHz BWs, respectively, and these are the highest amounts of isolation for a single antenna to best of our knowledge. The antenna with slot coupled Tx port provides more interport RF isolation as compared to single-layer antenna due to low coupling between slot coupled and co-planar quarter-wave microstrip fed ports. Both antenna structures have the capability to remove in-band nonlinear self-interference (SI) components without complex SI cancellation circuits.
CAY-1, a fungicidal saponin from<i>Capsicum</i>sp. fruit (2002)

Saponins are steroidal or terpenoid-based glycosides with surface active properties. A steroidal saponin, CAY-1, with a molecular weight of 1243.35 Da, was isolated and purified to homogeneity from commercially available dry, ground fruit of Capsicum frutescens. CAY-1 was shown to be a potent fungicide for the germinating conidia of Aspergillus flavus, A. fumigatus, A. parasiticus and A. niger with species-dependent LD90 values between 3 and 20 microM. Activity against some Aspergillus species was affected by the test medium used. In vitro assays, CAY-1 was effective against Pneumocystis carinii (IC50): 9.5 microM) and Candida albicans (IC90: 6.2 microM). CAY-1 had no effect on the viability of the nongerminating conidia of the two filamentous fungi, P. carinii and C. albicans, nor on the conidial type of Fusarium oxysporum. It was ineffective against the bacteria Enterobacter agglomerans, Bacillus subtilis, Escherichia coli and Staphylococcus aureus. CAY-1 was not cytotoxic to A 549 lung carcinoma cells or HeLa cells at effective fungicidal concentrations. The results indicate that CAY-1 is an effective fungicide for Aspergillus species, C. albicans and P. carinii at concentrations below the threshold for mammalian cell toxicity.
SAGMA: Secure Aggregation Grouped by Multiple Attributes (2020)

Encryption can protect data in outsourced databases -- in the cloud -- while still enabling query processing over the encrypted data. However, the processing leaks information about the data specific to the type of query, e.g., aggregation queries. Aggregation over user-defined groups using SQL's GROUP BY clause is extensively used in data analytics, e.g., to calculate the total number of visitors each month or the average salary in each department. The information leaked, e.g., the access pattern to a group, may reveal the group's frequency enabling simple, yet detrimental leakage-abuse attacks. In this work we present SAGMA -- an encryption scheme for performing secure aggregation grouped by multiple attributes. The querier can choose any combination of one or multiple attributes in the GROUP BY clause among the set of all grouping attributes. The encryption scheme only stores semantically secure ciphertexts at the cloud and query processing hides the access pattern, i.e., the frequency of each group. We implemented our scheme and our evaluation results underpin its practical feasibility.
Real‐Time Arrhythmia Identification from Automated Analysis of Intraatrial and Intraventricular Electrograms (1993)

Implantable cardioverter defibrillators have dramatically improved survival rates for patients at risk of sudden cardiac death, but the occurrence of inappropriate shocks remains an unresolved problem. Various means for better tachycardia detection, chiefly morphological analysis, have been proposed to address this problem. A new computerized scheme entitled Two-Channel Rate-Morphology (2CRM) was introduced. It is a real-time arrhythmia detection algorithm that combines timing and morphology information from intraatrial and intraventricular electrograms for arrhythmia diagnosis. The program 2CRM applies an initial cycle-by-cycle coding scheme followed by contextual diagnosis of underlying rhythm. The program was tested on 36 distinct passages of two-channel intracardiac signals from 30 patients. The distribution of the arrhythmias are as follows: 4 atrial fibrillation, 6 atrial flutter, 6 supraventricular tachycardia, 10 ventricular tachycardia, and 10 ventricular flutter-fibrillation. Of the analyzed 3,417 individual cardiac cycles 3,135 (91.7%) were correctly identified. Contextual diagnosis reversed 123 single-cycle errors to obtain a performance of 3,258 correct out of 3,417 (95.3%). Utilizing an uninterrupted continuous correct contextual diagnosis as indicator of successful arrhythmia detection, 2CRM obtained an accuracy of 34 out of 36 passages (94.4%).
Integrated On-Chip Inductors With Magnetic Films (2007)

On-chip inductors with 2 levels of magnetic material were integrated into an advanced 130-nm CMOS process to obtain over an order of magnitude increase in inductance (19times) and Q-factor (16times), significantly greater than prior values of les2.3times for high frequency inductors. The magnetic material enhances inductance at frequencies up to 9.8 GHz. Measurements and models of the permeability from amorphous CoZrTa alloy demonstrate that the skin effect and eddy current dampening become important. Two levels of magnetic material with high-temperature and long annealing-time stability, high saturation magnetization, low magnetostriction, high resistivity, minimal hysteretic loss, and compatibility with Si technology were used in combination with magnetic vias and elongated structures that take advantage of the uniaxial magnetic anisotropy
Use of Jack-up Drilling Units in Arctic Seas with Potential Ice Incursions during Open Water Season (2012)

Abstract Jack-up drilling units have been used in Arctic open water seasons and areaswith icebergs. They have not been used in areas where significant sea ice canmove in with high concentrations. These areas have typically been drilled usinga floating mobile offshore drilling unit (MODU) although the water depths aretypically less than 50 meters. Floating MODUs in shallow water depths can havesignificant downtime due to the limited offset in shallow water and typicallyrequire placing the well control equipment in a seabed cellar. In these areas, jack-ups can improve both operational safety and efficiency as they havelimited weather related downtime. Several studies were carried out to determine the feasibility of using amodern high capacity jack-up MODUs for exploratory drilling in these areas. This paper will review the studies including structural analysis, icemanagement approaches, and well control considerations. It will also review thefurther potential of jack-ups in the Arctic. Studies showed that using a jack-up drilling unit is feasible in shallowArctic seas such as the Chukchi Sea when coupled with an effective icemanagement system. The jack-up unit has sufficient ice resistance to withstandinteraction with thin early winter ice. Specific designs of jack-ups arecapable of taking impact forces from thicker ice floes that may occur during anice incursion event during the open water season. The maximum floe size duringan ice incursion is limited and controlled by the associated icemanagement system. An ice management system was developed using a combination of satelliteimagery, ice management vessels, and ice alert procedures. This system wasdetermined as effective in managing ice to allow the jack-up to operate in theChukchi Sea area. Environmental and personnel safety is enhanced by the use of aPre-positioned Capping Device, an in place source control device. The device isindependent from the rig's well control system and provides another level ofprotection in additional to the jack-up's BOP. The conclusion, based on structural and ice management studies, is thatmodern high capacity jack-up drilling units can be an effective way to drillwells during the open water season in shallow waters of Arctic seas includingareas in to which sea ice can move. The studies also show that there ispotential for use in other areas.
Modeling the PiezoElectronic Transistor - a nanoscale, strain-based transduction device for fast low power switching (2015)

We have invented a post-CMOS transduction device based on a piezoelectrically driven metal insulator transition termed the PiezoElectronic Transistor (PET) [1]. An input voltage pulse activates a piezoelectric element (PE) [2] which transduces input voltage into an electro-acoustic pulse that in turn drives an insulator to metal transition (IMT) in a piezoresistive element (PR) [3,4]; the transition efficiently transduces the electro-acoustic pulse to voltage. Using the known properties of bulk materials, we show using modeling that the PET achieves multi-GHz clock speeds with voltages as low as 0.1 V and a large On/Off switching ratio (≈10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> ) for digital logic [1]. The PET switch is compatible with CMOS-style logic. At larger scale the PET is predicted to function effectively as a large-area low voltage device for use in sensor applications and at larger yet as a RF-switch with an excellent figure of merit. Three demonstration devices have been fabricated to show proof of concept [5].
Photonic Switching of Native Ethernet Frames for Data Centers (2014)

We show new techniques of compression, scrambling, and packet size discrimination to implement a photonic-electronic hybrid switch that handle native Ethernet frames. The photonic switch is designed for a silicon photonic switch core.
Characterization of high index microsphere resonators in fiber-integrated microfluidic platforms (2011)

We investigate high-Q microsphere resonators with whispering gallery modes using a tapered optical microfiber immersed in a liquid inside a microfluidic platform. The strength of the coupling between the cavity and the microfiber taper is shown to depend on the contact position of the microsphere along the taper and on the refractive index contrast between the microsphere and the liquid environment. We demonstrate that barium titanate glass beads with index around 1.9 are promising candidates for developing sensor and optomechanical applications of such resonator systems.
Response and oligoclonal resistance to pembrolizumab in uterine leiomyosarcoma: Genomic, neoantigen, and immunohistochemical evaluation. (2016)

11043 Background: Predictive biomarkers for response and resistance to immune checkpoint blockade targeting programmed death 1 (PD-1) are incompletely characterized, and the utility of anti-PD-1 therapy for uterine leiomyosarcoma (ULMS) is unknown. Methods: A 49 yo woman with ULMS developed rapidly progressive metastatic disease 4 months after R1-resection of the primary tumor and was enrolled on a phase 1b study of pembrolizumab (10 mg/kg every 2 wks) (KEYNOTE-028). Tumor regression at multiple metastatic sites occurred within 2 months. A single pre-existing metastasis increased in size and was resected at 9 months. IHC, whole exome/transcriptome sequencing, and neoantigen analysis was performed on primary pretreatment (preRx) and treatment-resistant tumors (postRx). Results: Responsive tumor sites revealed complete pathologic response at time of surgery. Progressive tumor demonstrated viable ULMS. IHC showed tumor cells negative for PD-L1 and positive for PD-L2 both preRx and postRx. Degree of PD-1+ lymphocyte infiltration decreased significantly postRx compared to preRx. PreRx harbored exomic focal MYC amplification, TP53 nonsense mutation, and heterozygous PTEN deletion. PostRx maintained these genomic alterations and acquired a loss-of-function mutation in PTEN that resulted in biallelic PTEN inactivation. PreRx tumor expressed tumor-specific neoantigens (TSNs) that were immunogenic to patient-derived peripheral blood mononuclear cells; expression of TSNs decreased postRx. Conclusions: This patient exhibited complete pathologic response to pembrolizumab at all but one metastatic ULMS site. Genomic analysis of the resistant tumor revealed acquired bialllelic PTEN loss - recently implicated in resistance to PD-1 inhibition in melanoma and glioblastoma – reduced infiltration of PD-1+ lymphocytes, and diminished expression of neoantigens. To our knowledge, this is the first report of exceptional response to PD-1 inhibition in ULMS, and highlights biallelic PTEN loss and neoantigen downregulation as potential mechanisms of acquired resistance to immune checkpoint blockade across cancer types.