gebhart/patrepeval huggingface dataset:
Antioxidant supplementation and purification of semen for improved artificial insemination in livestock species (2014)

Improving sire reproductive performance in artificial insemination (AI) programs and maximizing the use of sires with valuable genomes are high on the list of priorities for livestock breeders in the United States and worldwide. While fixed-time AI and accurate estrous detection have already ameliorated the reproductive management of cows and sows, substantial gains remain to be made in the selection and utilization of male animals for field AI. In addition to better, more objective evaluation of breeding soundness and semen quality, numbers of spermatozoa per AI dose could be reduced and numbers of AI doses per collection could be increased without sacrificing conception rates if the fittest spermatozoa can be purified from raw semen and protected from adverse effects of dying and decaying spermatozoa present in both the fresh and the extended semen. The present article reviews recent progress in methodology for semen purification, including nanopurification and semen/extender supplementation with antioxidants.
Role of the Cys 2‐Cys 10 disulfide bond for the structure, stability, and folding kinetics of ribonuclease T1 (1994)

The Cys 2-Cys 10 disulfide bond in ribonuclease T1 was broken by substituting Cys 2 and Cys 10 by Ser and Asn, respectively, as present in ribonuclease F1. This C2S/C10N variant resembles the wild-type protein in structure and in catalytic activity. Minor structural changes were observed by 2-dimensional NMR in the local environment of the substituted amino acids only. The thermodynamic stability of ribonuclease T1 is strongly reduced by breaking the Cys 2-Cys 10 bond, and the free energy of denaturation is decreased by about 10 kJ/mol. The folding mechanism is not affected, and the trans to cis isomerizations of Pro 39 and Pro 55 are still the rate-limiting steps of the folding process. The differences in the time courses of unfolding and refolding are correlated with the decrease in stability: the folding kinetics of the wild-type protein and the C2S/C10N variant become indistinguishable when they are compared under conditions of identical stability. Apparently, the Cys 2-Cys 10 disulfide bond is important for the stability but not for the folding mechanism of ribonuclease T1. The breaking of this bond has the same effect on stability and folding kinetics as adding 1 M guanidinium chloride to the wild-type protein.
A novel pedestrian classification algorithm for a high definition dual camera 360 degrees surveillance system (2005)

In this paper a novel integrated multi-camera video-sensor (panoramic scene analysis - PSA) system is proposed for surveillance applications. In the proposed set-up, an omnidirectional imaging device is used in conjunction with a pan, tilt, zoom (PTZ) camera. In particular, the catadioptric sensor is calibrated and used in order to track and classify every single moving object within its 360-degree field of view. Classification is achieved by an innovative algorithm taking advantages from polar image and pedestrian geometrical properties. This approach greatly simplifies classification procedures and enhances target detection and locating system capabilities.
Dynamic field distributions of thin film inductive heads (1992)

Dynamic recording fields of thin-film inductive disk drive heads and the relationships to drive current, pole thickness, and pole materials have been investigated. Electron beam tomography was used to directly observe the recording fields. With Permalloy heads, improved frequency responses were achieved by exciting the magnetic core with higher drive currents. However, increases in the pole thickness significantly degraded the frequency responses. The amorphous CoTaZr head showed superior frequency response, and constant field intensity was maintained up to 30 MHz, regardless of drive current.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans (2021)

ABSTRACT Untargeted metabolomics via high-resolution mass spectrometry (HRMS) can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation (MS/MS) analysis, which uncovered more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and revealed that α-oxidation participates in metabolism of endogenous β-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.
Effect of a Rehabilitation Program After Mesenchymal Stromal Cell Transplantation for Advanced Osteonecrosis of the Femoral Head: A 10-Year Follow-Up Study (2022)

The 12-week rehabilitation program and annual follow-up after mesenchymal stromal cell transplantation for osteonecrosis of the femoral head was associated with pain reduction, maintaining hip muscle strength, widening range of motion, and improving quality of life. The level and timing of weight-bearing and social activity should be planned according to the individual's lifestyle and body composition.
Lyophobic (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
Towards Goal-Oriented Conformance Checking (2015)

Constructing a business process is important area between requirements engineering and business process management. Goal-oriented requirements analysis method is widely researched in requirements engineering and useful for reflecting organizational requirements to business process models, but actual business processes deviate from defined process models. Therefore, it is not sufficient for business process analysis only using model’s information. It is important to analyze actual conducted business process logged data. Analyzing business process logged data is called process mining and detecting differences between models and logs is called conformance checking. A lot of conformance checking approaches mainly focus on process aspects of business process, but this is not sufficient for analysis whether actual business processes can satisfy organizational goals. In this paper, we propose a goal-oriented conformance checking approach which can detect deviations between logs and models, and can analyze the effects of the deviation. It is useful for evaluation of the detected deviation. We represent the effectiveness of our approach conducting a case study using the publicly available log.
ChemInform Abstract: Co‐Catalyzed Mild and Chemoselective Reduction of Phenyl Esters with NaBH4: A Practical Synthesis of (R)‐Tolterodine. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Glucose kinetics during a meal: one vs two compartment minimal model (2002)

During IVGTT the two compartment model performs better than the single compartment one. Here the aim is to test 1 vs 2 compartment model during a more gentle perturbation such an oral test. 1 and 2 compartment minimal model, both unlabeled and labeled, were identified with glucose rate of appearance, i.e. the input of the model, assumed known from a model-independent method. For unlabeled data both models perform similarly while for labeled data the 2 compartment model is better. Among model-based metabolic indices differences were noted in the inhibition of endogenous glucose production due to glucose itself predicted by one and two compartment models.
A General Model for Preferential Hetero-oligomerization of LIN-2/7 Domains (2005)

LIN-2/7 (L27) domains are protein interaction modules that preferentially hetero-oligomerize, a property critical for their function in directing specific assembly of supramolecular signaling complexes at synapses and other polarized cell-cell junctions. We have solved the solution structure of the heterodimer composed of the L27 domains from LIN-2 and LIN-7. Comparison of this structure with other L27 domain structures has allowed us to formulate a general model for why most L27 domains form an obligate heterodimer complex. L27 domains can be divided in two types (A and B), with each heterodimer comprising an A/B pair. We have identified two keystone positions that play a central role in discrimination. The residues at these positions are energetically acceptable in the context of an A/B heterodimer, but would lead to packing defects or electrostatic repulsion in the context of A/A and B/B homodimers. As predicted by the model, mutations of keystone residues stabilize normally strongly disfavored homodimers. Thus, L27 domains are specifically optimized to avoid homodimeric interactions.
Supplemental Figure 5 from ADCT-301, a Pyrrolobenzodiazepine (PBD) Dimer–Containing Antibody–Drug Conjugate (ADC) Targeting CD25-Expressing Hematological Malignancies (2023)

&lt;p&gt;In vivo efficacy in Karpas disseminated models. Kaplan Meier survival plots of disseminated Karpas 299 models&lt;/p&gt;
Flux-tunable heat sink for quantum electric circuits (2018)

Superconducting microwave circuits show great potential for practical quantum technological applications such as quantum information processing. However, fast and on-demand initialization of the quantum degrees of freedom in these devices remains a challenge. Here, we experimentally implement a tunable heat sink that is potentially suitable for the initialization of superconducting qubits. Our device consists of two coupled resonators. The first resonator has a high quality factor and a fixed frequency whereas the second resonator is designed to have a low quality factor and a tunable resonance frequency. We engineer the low quality factor using an on-chip resistor and the frequency tunability using a superconducting quantum interference device. When the two resonators are in resonance, the photons in the high-quality resonator can be efficiently dissipated. We show that the corresponding loaded quality factor can be tuned from above 10<sup>5</sup> down to a few thousand at 10 GHz in good quantitative agreement with our theoretical model.
BGP Prefix Segment in Large-Scale Data Centers (2019)

This document describes the motivation and benefits for applying
segment routing in BGP-based large-scale data-centers. It describes
the design to deploy segment routing in those data-centers, for both
the MPLS and IPv6 dataplanes.
CD44‐positive colorectal adenoma cells express the potential stem cell markers musashi antigen (msi1) and ephrin B2 receptor (EphB2) (2007)

The majority of colorectal adenomas contain a mutation in the APC gene activating the wnt pathway. As wnt signalling preserves stem cell functions, it would be expected that stem cells would be enriched in adenomas. We have shown expression of the wnt target gene CD44, which may characterize the expanded stem cell compartment, in colorectal tumours. To investigate this possibility, we performed an immunohistological survey of CD44 expression in relation to the proliferation marker Ki67 and apoptosis in colorectal tumour tissue, and have isolated a CD44-positive subpopulation of the human colorectal adenoma cell line LT97 for cell biological analysis. In tissues, CD44 expression was not related to Ki67, but was associated with lower apoptosis in the CD44-positive areas. CD44-positive and -negative populations isolated from LT97 cultures were identical in their Ki-ras and p53 status but differed in their growth and survival characteristics. While CD44-positive cells attached and grew to reconstitute the original culture, the CD44-negative cells rapidly underwent apoptosis and were unable to resume growth. In comparison to unsorted growing LT97 cells, the CD44-positive cells had shifted beta-catenin into the nucleus and expressed beta-catenin target genes, such as ephrin B receptor (ephB2) and musashi antigen (msi1). By contrast, CD44-negative cultures contained no cells with nuclear beta-catenin. In summary, the CD44-positive cells accumulating in colorectal tumours have increased survival capacity both in vivo and in vitro. They also express markers typical of colorectal progenitor cells, msi1 and ephB2, in the premalignant progenitor population.
Data from RLY-4008, the First Highly Selective FGFR2 Inhibitor with Activity across <i>FGFR2</i> Alterations and Resistance Mutations (2023)

&lt;div&gt;Abstract&lt;p&gt;Oncogenic activation of fibroblast growth factor receptor 2 (FGFR2) drives multiple cancers and represents a broad therapeutic opportunity, yet selective targeting of FGFR2 has not been achieved. Although the clinical efficacy of pan-FGFR inhibitors (pan-FGFRi) validates &lt;i&gt;FGFR2&lt;/i&gt; driver status in &lt;i&gt;FGFR2&lt;/i&gt; fusion–positive intrahepatic cholangiocarcinoma, their benefit is limited by incomplete target coverage due to FGFR1- and FGFR4-mediated toxicities (hyperphosphatemia and diarrhea, respectively) and the emergence of &lt;i&gt;FGFR2&lt;/i&gt; resistance mutations. RLY-4008 is a highly selective, irreversible FGFR2 inhibitor designed to overcome these limitations. &lt;i&gt;In vitro&lt;/i&gt;, RLY-4008 demonstrates &gt;250- and &gt;5,000-fold selectivity over FGFR1 and FGFR4, respectively, and targets primary alterations and resistance mutations. &lt;i&gt;In vivo&lt;/i&gt;, RLY-4008 induces regression in multiple xenograft models—including models with &lt;i&gt;FGFR2&lt;/i&gt; resistance mutations that drive clinical progression on current pan-FGFRi—while sparing FGFR1 and FGFR4. In early clinical testing, RLY-4008 induced responses without clinically significant off-isoform FGFR toxicities, confirming the broad therapeutic potential of selective FGFR2 targeting.&lt;/p&gt;Significance:&lt;p&gt;Patients with &lt;i&gt;FGFR2&lt;/i&gt;-driven cancers derive limited benefit from pan-FGFRi due to multiple FGFR1–4-mediated toxicities and acquired &lt;i&gt;FGFR2&lt;/i&gt; resistance mutations. RLY-4008 is a highly selective FGFR2 inhibitor that targets primary alterations and resistance mutations and induces tumor regression while sparing other FGFRs, suggesting it may have broad therapeutic potential.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-23-0728" target="_blank"&gt;See related commentary by Tripathi et al., p. 1964&lt;/a&gt;.&lt;/i&gt;&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-13-9-ITI" target="_blank"&gt;This article is featured in Selected Articles from This Issue, p. 1949&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Synthesis and Antiviral Evaluation of the β-L-Enantiomers of Some Thymine 3′-Deoxypentofuranonucleoside Derivatives (2000)

3'-Deoxy-beta-L-erythro- (3), 3'-deoxy-beta-L-threo- (6), 2'-fluoro- (7) and 2'-azido-2',3'-dideoxy-beta-L-erythro- (10) pentofuranonucleoside derivatives of thymine have been synthesized and their antiviral properties examined. All these derivatives were stereospecifically prepared by glycosylation of thymine with a suitable peracylated 3-deoxy-L-erythro-pentofuranose sugar (1), followed by appropriate chemical modifications. The prepared compounds were tested for their activity against HIV, but they did not show an antiviral effect.
Detection of Quiescent Radioresistant Epithelial Progenitors in the Adult Thymus (2017)

Thymic aging precedes that of other organs and is initiated by the gradual loss of thymic epithelial cells (TECs). Based on <i>in vitro</i> culture and transplantation assays, recent studies have reported on the presence of thymic epithelial progenitor cells (TEPCs) in young adult mice. However, the physiological role and properties of TEPC populations reported to date remain unclear. Using an <i>in vivo</i> label-retention assay, we previously identified a population of quiescent but non-senescent TECs. The goals of this study were therefore (i) to evaluate the contribution of these quiescent TECs to thymic regeneration following irradiation-induced acute thymic injury and (ii) to characterize their phenotypic and molecular profiles using flow cytometry, immunohistology, and transcriptome sequencing. We report that while UEA1<sup>+</sup> cells cycle the most in steady state, they are greatly affected by irradiation, leading to cell loss and proliferative arrest following acute thymic involution. On the opposite, the UEA1<sup>-</sup> subset of quiescent TECs is radioresistant and proliferate <i>in situ</i> following acute thymic involution, thereby contributing to thymic regeneration in 28- to 30-week-old mice. UEA1<sup>-</sup> quiescent TECs display an undifferentiated phenotype (co-expression of K8 and K5 cytokeratins) and express high levels of genes that regulate stem cell activity in different tissues (e.g., <i>Podxl</i> and <i>Ptprz1</i>). In addition, two features suggest that UEA1<sup>-</sup> quiescent TECs occupy discrete stromal niches: (i) their preferential location in clusters adjacent to the cortico-medullary junction and (ii) their high expression of genes involved in cross talk with mesenchymal cells. The ability of UEA1<sup>-</sup> quiescent TECs to participate to TEC regeneration qualifies them as <i>in vivo</i> progenitor cells particularly relevant in the context of regeneration following acute thymic injury.
Structure-Based Super-Resolution Recovery of Three-Photon Quantum States\n from Two-Fold Coincidences (2014)

The field of quantum information has been growing fast over the past decade.\nOptical quantum computation, based on the concepts of KLM and cluster states,\nhas witnessed experimental realizations of larger and more complex systems in\nterms of photon number. Quantum optical systems, which offer long coherence\ntimes and easy manipulation of single qubits, allow us to probe quantum\nproperties of the light itself and of the physical systems around it. Recently,\na linear scheme for quantum computing, relying on the bosonic nature of\nparticles, has been proposed and realized experimentally with photons. The\nability to efficiently measure superpositions of quantum states consisting of\nseveral photons is essential to the characterization of such systems. In fact,\nthe entire field of quantum information completely relies on the ability to\nrecover quantum states from measurements. However, the characterization of\nquantum states requires many measurements, and often necessitates complicated\nmeasurements schemes; for example, characterizing qubits requires measurements.\nHere, we utilize structure, inherent to physically interesting quantum states\nof light, in order to reduce the complexity in the recovery of a quantum state.\nIn particular, we devise a method enabling the recovery of three-photon quantum\nstates from only two-fold correlation measurements in a single setting. The\nability to take two-fold coincidences instead of three-fold offers the recovery\nof the quantum states in far less measurements and in a considerably higher\nSNR, because detection of two-photon events is much more likely than that of\nthree-photon ones. The concept suggested here paves the way to further ideas on\nstructure-based super resolution in quantum state tomography, such as\nrecovering a quantum state in an unknown basis in a single setup and recovering\nthe state of several photons without number resolving detectors.\n
The effect of Mg-doping and Cu nonstoichiometry on the photoelectrochemical response of CuFeO2 (2016)

We report the tuning of CuFeO<sub>2</sub> photoelectrodes by Mg doping and Cu deficiency to demonstrate the effects of carrier concentration on the photoresponse.
Dosimetry Prediction for Clinical Translation of 64Cu-Pembrolizumab ImmunoPET Targeting Human PD-1 Expression (2018)

The immune checkpoint programmed death 1 receptor (PD-1) expressed on some tumor-infiltrating lymphocytes, and its ligand (PD-L1) expressed on tumor cells, enable cancers to evade the immune system. Blocking PD-1 with the monoclonal antibody pembrolizumab is a promising immunotherapy strategy. Thus, noninvasively quantifying the presence of PD-1 expression in the tumor microenvironment prior to initiation of immune checkpoint blockade may identify the patients likely to respond to therapy. We have developed a <sup>64</sup>Cu-pembrolizumab radiotracer and evaluated human dosimetry. The tracer was utilized to image hPD-1 levels in two subcutaneous mouse models: (a) 293 T/hPD-1 cells xenografted into NOD-scid IL-2Rγnull mice (NSG/293 T/hPD-1) and (b) human peripheral blood mononuclear cells engrafted into NSG bearing A375 human melanoma tumors (hNSG/A375). In each mouse model two cohorts were evaluated (hPD-1 blockade with pembrolizumab [blk] and non-blocked [nblk]), for a total of four groups (n = 3-5/group). The xenograft-to-muscle ratio in the NSG/293 T/hPD-1 model at 24 h was significantly increased in the nblk group (7.0 ± 0.5) compared to the blk group (3.4 ± 0.9), p = 0.01. The radiotracer dosimetry evaluation (PET/CT ROI-based and ex vivo) in the hNSG/A375 model revealed the highest radiation burden to the liver. In summary, we validated the <sup>64</sup>Cu-pembrolizumab tracer's specific hPD-1 receptor targeting and predicted human dosimetry.