gebhart/patrepeval huggingface dataset:
Transmission of Bovine Viral Diarrhea Virus from Persistently Infected Cattle to Pregnant White-tailed Deer (2008)

Substantial impact of bovine viral diarrhea virus (BVDV) on the cattle industries has prompted introduction of organized control programs in many states. These programs primarily focus on identification and removal of persistently infected (PI) cattle, the main source of BVDV transmission. In addition to cattle, BVDV may infect a large number of species within the order Artiodactyla as demonstrated by seropositivity. The white-tailed deer is the most abundant wild ruminant species in North America and BVDV infection has been documented in this species. Recently, experimental inoculation of pregnant white-tailed deer resulted in the birth of a persistently infected fawn. Considering the role of PI cattle in the maintenance of BVDV within cattle populations, PI white-tailed deer that harbor and shed the virus continuously may hamper successful execution of control efforts. The objective of this study was the investigation of interspecific BVDV transmission by cohabitation of PI cattle with pregnant white-tailed deer.
Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes (2022)

ABSTRACT Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (234 individuals), generated using the Illumina 450K or EPIC microarray. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differential methylated loci across FTLD subgroups/subtypes. Additionally, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5’UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. Additionally, in the three independent co-methylation networks, OTUD4 -containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.
A New Molecular Theory of Non-Linear Viscoelasticity for Vitrifiable (or Crystallizable) Thermoplastic Polyurethane Elastomers (2002)

The molecular theory of non-linear viscoelasticity for vitrifiable thermoplastic polyurethane elastomers (VTPUE) is a refinement and extension of viscoelastic theory of thermoplastic elastomers and polyurethanes to glassy transition, a structural model and a mechanism of vitrification for glassy polymers were proposed. Five kinds of constituent chains with Nagai chain constraint consisting of soft-domains, hard-domains, and entanglements are used as the elementary structural and statistical ensemble units for the correlation of molecular and phase-domain structures to the static and dynamic mechanical behaviors. So the influences of non-Gaussian in character, the phase separation of domain, the network topology of structure, the affined deformation of constituent chains, and the thermal history are all taken into account in the constituent chains of the theory. Free energies of deformation for the VTPUE segment copolymer were calculated by the statistical mechanics with the probability distribution functions of the sizes for the five kinds of constituent chains. Then the static constitutive equations and modulus of four types of deformation and the dynamic shear viscosity, modulus and loss tangent of VTPUE are derived from the proposed theory. The theory is successful in relating the molecular chain parameters C100, C020, and C200 to the constitutive equations and modulus under large deformations and the micro-domain structure to the complex shear viscosity and modulus and the loss tangent. The dynamic shear modulus and loss tangent of VTPUE are related to the domain structures through the fraction of hard segments (Wh), the molecular weight of soft segment (Mns), and the growth dimensional parameters of hard and soft domains (β). Two series of linear VTPUE copolymers (ES and ET) with different fractions(Wh) of hard segments and molecular weight (Mns) of soft segments were prepared. Their static and dynamic mechanical properties were studied by uni-axial extension and dynamic analysis tests. Then the constitutive equation at uni-axial extension and the expressions of shear modulus and loss tangent are verified by these experimental data, and excellent agreement between the theory and experiments is achieved. It is shown, that the proposed theory can predict the viscoelastic behavior of vitrifiable thermoplastic polyurethanes.
Improvement technique for Power Efficiency of DAB DC-DC Converters by Reducing Hard Switching and Copper Losses in Light Loads (2023)

Dual active bridge (DAB) converters have many advantages, such as bidirectional power transfer, and are becoming popular in energy storage systems such as microgrids. However, if the input-output voltage conversion ratio is not equal to the turn ratio of the magnetic transformer, the power efficiency at light loads deteriorates. While hard switching has attracted attention as a cause of this power efficiency deterioration, this paper shows that in addition to hard switching, part of the copper loss during conventional operation becomes a fixed loss, causing efficiency deterioration at light loads. As for the solution technique of this problem, we propose the control switching technique using triangular current control in buck mode and trapezoidal current control in boost mode, respectively. The experimental results have confirmed that power efficiency can be improved by up to 25% with triangular current control at an input-output voltage conversion ratio of 100V/75V and by up to 20% with trapezoidal current control at an input-output voltage conversion ratio of 100V/125V.
Pathogenesis of genetic haemochromatosis (1993)

Genetic haemochromatosis is an autosomal recessive inherited iron overload disease. The genetic defect and the underlying metabolic error are not known. Several observations indicate that the 2-4-fold increase of iron absorption is due to a regulatory defect of a membrane iron transport system in duodenal mucosal cells. The key pathophysiologic factor may be the increase of gut-derived non-transferrin bound iron liganded to low-molecular mass organic molecules. A putative membrane carrier protein for non-transferrin bound iron was identified and preliminary data suggest its enrichment in plasma membranes of human mucosal cells as well as in liver and other organs which are affected in genetic haemochromatosis. Cellular accumulation of ionic iron leads to peroxidative decomposition of organelle membrane phospholipids with the consequence of cell degeneration and cell death. Impairment of organ function and structural alterations such as cirrhosis of the liver are clinical manifestations.
Work in progress - Developing transversal skills in an online theoretical engineering subject (2007)

In some concentration subjects of online programs, such as theoretical scientific subjects (Mathematics, Physics, etc), where most of the problems have only one solution and there are few chances for discussion, the development of transversal skills, such as team-working, leadership, or oral and written expression is forgotten. Typically, only specific competences about the subject are acquired. Due to the lack of discussions, students usually work in an autonomous way, only a few days before the exam, and this causes a high ratio of desertion. To avoid this, teamwork has been planned. In it, lecturers and students assess the correctness of the solutions, the presentation of the reports, the written expression, the pedagogical quality of their explanations, and some teamwork skills such as organization, distribution of the work, the use of e-learning tools for communication, etc. To collect and analyze the marks which students grade each other's work a simple tool has been created. This way, in a preliminary analysis it is shown that students are closer to their mates, they develop transversal skills, and they study during all the year, increasing the ratio of success.
Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate (2009)

We identified a cis-prenyltransferase gene, neryl diphosphate synthase 1 (NDPS1), that is expressed in cultivated tomato (Solanum lycopersicum) cultivar M82 type VI glandular trichomes and encodes an enzyme that catalyzes the formation of neryl diphosphate from isopentenyl diphosphate and dimethylallyl diphosphate. mRNA for a terpene synthase gene, phellandrene synthase 1 (PHS1), was also identified in these glands. It encodes an enzyme that uses neryl diphosphate to produce beta-phellandrene as the major product as well as a variety of other monoterpenes. The profile of monoterpenes produced by PHS1 is identical with the monoterpenes found in type VI glands. PHS1 and NDPS1 map to chromosome 8, and the presence of a segment of chromosome 8 derived from Solanum pennellii LA0716 causes conversion from the M82 gland monoterpene pattern to that characteristic of LA0716 plants. The data indicate that, contrary to the textbook view of geranyl diphosphate as the "universal" substrate of monoterpene synthases, in tomato glands neryl diphosphate serves as a precursor for the synthesis of monoterpenes.
High Speed Instrumentation for Inspection of transparent parts (2013)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.
Improved Recursive DNS Server Selection for Multi-Interfaced Nodes (2012)

A multi-interfaced node is connected to multiple networks, some of which might be utilizing private DNS namespaces.A node commonly receives recursive DNS server configuration information from all connected networks.Some of the recursive DNS servers might have information about namespaces other servers do not have.When a multi-interfaced node needs to utilize DNS, the node has to choose which of the recursive DNS servers to use.This document describes DHCPv4 and DHCPv6 options that can be used to configure nodes with information required to perform informed recursive DNS server selection decisions.
Tri‐halide vapor phase epitaxy of GaN using GaCl3 gas as a group III precursor (2011)

Abstract Tri‐halide vapor phase epitaxy (THVPE) of GaN using GaCl 3 gas generated by the reaction between metallic Ga and Cl 2 gas at the source zone was investigated. From thermodynamic analysis, it was predicted that the driving force for GaN growth by THVPE would be larger than that by conventional mono halide vapor phase epitaxy (HVPE) using GaCl as a group III precursor. From the growth experiments, it was shown that the growth rate of GaN by THVPE was much higher than that by conventional HVPE under the same input partial pressure conditions. It was also revealed that GaN growth is possible at higher temperatures by THVPE. In photoluminescence (PL) and X‐ray diffraction (XRD) measurements, a GaN layer grown by THVPE at 1150 °C has optical properties and crystalline quality superior to that of a GaN layer grown by HVPE at 970 °C (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Advances in 2D boron nitride nanostructures: nanosheets, nanoribbons, nanomeshes, and hybrids with graphene (2012)

The recent surge in graphene research has stimulated interest in the investigation of various 2-dimensional (2D) nanomaterials. Among these materials, the 2D boron nitride (BN) nanostructures are in a unique position. This is because they are the isoelectric analogs to graphene structures and share very similar structural characteristics and many physical properties except for the large band gap. The main forms of the 2D BN nanostructures include nanosheets (BNNSs), nanoribbons (BNNRs), and nanomeshes (BNNMs). BNNRs are essentially BNNSs with narrow widths in which the edge effects become significant; BNNMs are also variations of BNNSs, which are supported on certain metal substrates where strong interactions and the lattice mismatch between the substrate and the nanosheet result in periodic shallow regions on the nanosheet surface. Recently, the hybrids of 2D BN nanostructures with graphene, in the form of either in-plane hybrids or inter-plane heterolayers, have also drawn much attention. In particular, the BNNS-graphene heterolayer architectures are finding important electronic applications as BNNSs may serve as excellent dielectric substrates or separation layers for graphene electronic devices. In this article, we first discuss the structural basics, spectroscopic signatures, and physical properties of the 2D BN nanostructures. Then, various top-down and bottom-up preparation methodologies are reviewed in detail. Several sections are dedicated to the preparation of BNNRs, BNNMs, and BNNS-graphene hybrids, respectively. Following some more discussions on the applications of these unique materials, the article is concluded with a summary and perspectives of this exciting new field.
Base Composition Profiling of Human Mitochondrial DNA Using Polymerase Chain Reaction and Direct Automated Electrospray Ionization Mass Spectrometry (2009)

We describe an automated system for high-resolution profiling of human mitochondrial DNA (mtDNA) based upon multiplexed polymerase chain reaction (PCR) followed by desolvation and direct analysis using electrospray ionization mass spectrometry (PCR/ESI-MS). The assay utilizes 24 primer pairs that amplify targets in the mtDNA control region, including the hypervariable regions typically sequenced in a forensic analysis. Profiles consisting of product base compositions can be stored in a database, compared to each other, and compared to sequencing results. Approximately 94% of discriminating information obtained by sequencing is retained with this technique. The assay is more discriminating than sequencing minimum HV1 and HV2 regions because it interrogates more of the mitochondrial genome. A profile compared to a population database can be subjected to the same statistics used for assessing the significance of concordant mtDNA sequences. The assay is not hindered by length heteroplasmy, can directly analyze template mixtures, and has a sensitivity of <25 pg of total DNA per reaction. Analysis of 3331 independent trials of the same sample over 28 months produced an average mass measurement uncertainty of 10.1 +/- 8.0 ppm, with >99% of trials producing a full profile with automated analysis. The technique has direct application to analysis of forensic biological evidence.
Supplementary Figure 3 from Development of an Fc-Enhanced Anti–B7-H3 Monoclonal Antibody with Potent Antitumor Activity (2023)

&lt;p&gt;PDF file, 89KB, Measurement of IL-5 (Panel A), IL-6 (Panel B) and TNF-B (Panel C) cytokine levels in serum samples collected from cynomolgus monkeys prior to infusion (Pre) or at the indicated time points following intravenous administration of PBS vehicle (Day 1) or MGA271 at the indicated dose (Day 8). The top two panels of each cytokine data set represent all animals (N=6) in each dosing group, while the bottom three panels represent only the recovery group animals (N=2) in each dosing group. Sera from the samples were analyzed for cytokine levels using the Becton Dickinson Cytometric Bead Array Non-Human Primate Th1/Th2 Cytokine kit.&lt;/p&gt;
Invasive Gastrointestinal and Cutaneous Mucormycosis in Deceased Donor Small Bowel Transplantation: Case Report and Review of Literature (2009)

Fungal infection is an uncommon complication after small bowel transplantation. We present a rare form of mucormycosis found in the small bowel graft and in the skin of a recipient. We reviewed chart data and performed MEDLINE searches and found that this case was the first to report 2 kinds of mucormycosis to be found after organ transplantation. The patient was a 12 month old female baby who underwent small bowel transplantation due to short bowel syndrome. After 12 days she experienced acute cellular rejection which responded to steroid. 6 days later due to sustained fever, poor feeding and abdominal distention endoscopic biopsy was done which revealed mucormycosis. Antifungal treatment with lipo-amphotericin B was initiated, yet there was no improvement of clinical symptoms. On the 23 post operative day a black eschar developed on the incision site of the skin and biopsy was done which revealed cutaneous mucormycosis. Infected skin debridement and graftectomy was done but our patient expired because of septic shock.
Position Information From Reflecting Surfaces (2021)

In the context of positioning an agent with a single-anchor, this contribution focuses on the Fisher information about the position, orientation and clock offset of the agent provided by single-bounce reflections. The availability of prior knowledge of the agent's environment is taken into account via a prior distribution of the position of virtual anchors, and the rank, intensity and direction of provided information is studied. We show that when no prior knowledge is available, single-bounce reflections offer position information in the direction parallel to the reflecting surface, irrespective of the agent's and anchor's locations. We provide a geometrically intuitive explanation of the results and present numerical examples demonstrating their potential implications.
Nutritional and tissue-specific regulation of cytochrome P450 CYP711AMAX1homologues and strigolactone biosynthesis in wheat (2023)

Strigolactones (SLs) are a class of phytohormones regulating branching/tillering, and their biosynthesis has been associated with nutritional signals and plant adaptation to nutrient-limiting conditions. The enzymes in the SL biosynthetic pathway downstream of carlactone are of interest as they are responsible for structural diversity in SLs, particularly cytochrome P450 CYP711A subfamily members, such as MORE AXILLARY GROWTH1 (MAX1) in Arabidopsis. We identified 13 MAX1 homologues in wheat, clustering in four clades and five homoeologous subgroups. The utilization of RNA-sequencing data revealed a distinct expression pattern of MAX1 homologues in above- and below-ground tissues, providing insights into the distinct roles of MAX1 homologues in wheat. In addition, a transcriptional analysis showed that SL biosynthetic genes were systematically regulated by nitrogen supply. Nitrogen limitation led to larger transcriptional changes in the basal nodes than phosphorus limitation, which was consistent with the observed tillering suppression, as wheat showed higher sensitivity to nitrogen. The opposite was observed in roots, with phosphorus limitation leading to stronger induction of most SL biosynthetic genes compared with nitrogen limitation. The observed tissue-specific regulation of SL biosynthetic genes in response to nutritional signals is likely to reflect the dual role of SLs as rhizosphere signals and branching inhibitors.
Dysfunction of oesophageal motility in Helicobacter pylori‐infected patients with reflux oesophagitis (2001)

Among patients with a similar degree of reflux oesophagitis, H. pylori-infected patients have more severe oesophageal dysmotility and lower oesophageal sphincter dysfunction. Oesophageal motor dysfunction probably plays a dominant role in the development of gastro-oesophageal reflux disease in patients with H. pylori infection.
Analysis of Synchronization Impairments for Cooperative Base Stations Using OFDM (2015)

Base station cooperation is envisioned as a key technology for future cellular networks, as it has the potential to eliminate intercell interference and to enhance spectral efficiency. To date, there is still lack of understanding of how imperfect carrier and sampling frequency synchronization between transmitters and receivers limit the potential gains and what the actual system requirements are. In this paper, OFDM signal model is established for multiuser multicellular networks, describing the joint effect of multiple carrier and sampling frequency offsets. It is shown that the impact of sampling offsets is much smaller than the impact of carrier frequency offsets. The model is extended to the downlink of base-coordinated networks and closed-form expressions are derived for the mean power of users’ self-signal, interuser, and intercarrier interference, whereas it is shown that interuser interference is the main source of degradation. The SIR is inverse to the base stations’ carrier frequency variance and to the square of time since the last precoder update, whereas it grows with the number of base stations and drops with the number of users. Through user selection, the derived SIR upper bound can be approached. Finally, system design recommendations for meeting synchronization requirements are provided.
Tissue imaging using optical projection tomographic microscopy (2014)

Conventional Optical Projection Tomography (OPT) can image tissue samples both in absorption and fluorescence mode. Absorption image can show the anatomical structure of the sample, while fluorescence mode can determine specific molecular distribution. The depth of focus (DOF) of the lens in conventional OPT needs to transverse the whole sample. As a result, resolution will be poor due to the low numerical aperture (NA) needed to generate large DOF. In conventional pathology, the specimens are embedded in wax and sliced into thin slices so that high NA objective lens can be used to image the sections. In this case, the high resolution is obtained by using high NA objective lens, but 3D images can be only obtained by stitching different sections together. Here, we propose a new method that can image entire specimen without sectioning with the same high resolution as the conventional pathology. To produce high resolution that is isotropic, the original OPTM system scans the focal plane of the high NA objective through the entire specimen to produce one projection image. Then the specimen is rotated so that the subsequent projection is taken at different perspective. After all the projections are taken, 3D images are generated by the filtered back-projection method. However, the scanning rate is limited by scanning objective lens due to the large mass of the lens. Here we show a new OPTM system that scans the mirror in the conjugate image space of the object to produce projections.