gebhart/patrepeval huggingface dataset:
Coordinate expression of the three zona pellucida genes during mouse oogenesis (1995)

The mammalian zona pellucida is an extracellular matrix that surrounds growing oocytes, ovulated eggs and early embryos. The mouse zona is composed of three sulfated glycoproteins: ZP1, ZP2 and ZP3. Each is critically involved in fertilization, the postfertilization block to polyspermy and protection of the preimplantation embryo. We have previously isolated cDNAs encoding mouse ZP2 and ZP3 and now report the isolation of a full-length cDNA encoding ZP1. Mouse ZP1 is composed of a 623 amino acid polypeptide chain with a signal peptide and a carboxyl terminal transmembrane domain, typical of all zona proteins. Sequence comparison demonstrate that mouse ZP1 is an orthologue of a rabbit zona protein, R55. The expression of R55 has been reported previously in both oocytes and granulosa cells. However, by northern analysis and in situ hybridization with 33P-labelled antisense probes to each of the three mouse zona mRNAs, we have determined that the expression of each mouse zona gene is restricted to the oocyte. ZP2 transcripts, but not ZP1 or ZP3, are detected in resting (15 microns diameter) oocytes, and all three zona transcripts coordinately accumulate as oocytes begin to grow. Together they represent approximately 1.5% of the total poly(A)+ RNA in 50-60 microns oocytes. In the latter stages of oogenesis, their abundance declines and each zona transcript is present in ovulated eggs at less than 5% of its maximal level. No zona transcripts were detected above background signal in granulosa cells. We conclude that, in mice, the three zona pellucida genes are expressed in a coordinate, oocyte-specific manner during the growth phase of oogenesis. Our data support the hypothesis that the transcription of the zona genes is controlled, in part, by shared regulatory element(s).
Antimicrobial and Chemotactic Activity of Scorpion-Derived Peptide, ToAP2, against Mycobacterium massiliensis (2018)

<i>Mycobacterium massiliense</i> is a rapid growing, multidrug-resistant, non-tuberculous mycobacteria that is responsible for a wide spectrum of skin and soft tissue infections, as well as other organs, such as the lungs. Antimicrobial peptides had been described as broad-spectrum antimicrobial, chemotactic, and immunomodulator molecules. In this study we evaluated an antimicrobial peptide derived from scorpion <i>Tityus obscurus</i> as an anti-mycobacterial agent in vitro and in vivo. Bioinformatics analyses demonstrated that the peptide ToAP2 have a conserved region similar to several membrane proteins, as well as mouse cathelicidin. ToAP2 inhibited the growth of four <i>M. massiliense</i> strains (GO01, GO06, GO08, and CRM0020) at a minimal bactericidal concentration (MBC) of 200 µM. MBC concentration used to treat infected macrophages was able to inhibit 50% of the bacterial growth of all strains. ToAP2 treatment of infected mice with bacilli reduced the bacterial load in the liver, lung, and spleen, similarly to clarithromycin levels (90%). ToAP2 alone recruited monocytes (F4/80<sup>low</sup> Gr1), neutrophils (F4/80<sup>-</sup> Gr1), and eosinophils (F4/80+ Gr1+). ToAP2, together with <i>M. massiliense</i> infection, was able to increase F4/80<sup>low</sup> and reduce the percentage of F4/80<sup>high</sup> macrophages when compared with infected and untreated mice. ToAP2 has in vitro anti-microbial activity that is improved in vivo due to chemotactic activity.
Design and modeling of a microwave imaging system for breast cancer detection (2015)

The main focus of the present paper is the design and construction of a microwave-imaging system prototype for use in research towards early breast cancer detection. To design and optimize the proposed system prototype, in particular to model the wideband antenna that acts as transmitter/receiver, a finite element method (FEM) approach is used. For signals generation and acquisition, low-cost yet high-precision off-the-shelf components replace a costly vector network analyzer (VNA). Even though the prototype is still under development, the agreement between simulations and measurements, the comparison with a reference VNA, and the validation with a commercial solver (FEKO) are encouraging.
Narratives of Black Women STEM Faculty: Breaking Barriers to Promote Institutional Transformation at Historically Black Colleges and Universities (2022)

Women faculty at Historically Black Colleges and Universities (HBCUs), experience many barriers. HBCUs’ rich histories of advancing racial equity have often outweighed a focus on gender equity, with issues at the intersection of race and gender receiving minimal attention. This study highlights the need for institutional transformation at HBCUs by identifying the structural factors that promote and inhibit Black women STEM faculty advancement. Interviews (n=15) were conducted with HBCU Black women STEM faculty using the Life Interview approach. The three major themes related to barriers included: (1) greater likelihood of having their expertise questioned, (2) increased pressure to work harder, and (3) sexism, racism, and gendered racism. This study expands upon existing research in the literature by focusing on an understudied population, Black women STEM faculty at HBCUs. Findings suggest that to advance institutional transformation diversity, equity, and inclusion goals, colleges and universities must establish infrastructures that include supports of benefit to the professional advancement of all faculty.
Comparison of Endmill Tool Coating Performance during Machining of Ti6Al4V Alloy (2014)

Titanium is a hard-to-machine material. An improvement in tool life via advanced tool coating materials can lead to higher productivity of titanium. In this study, a Grade 5 Ti workpiece was milled using a diamond-like carbon coated (ta-C) cutting tool and its performance compared with the standard TiAlN coated endmill. It was found that a ta-C coated tool experienced higher cutting forces than the TiAlN coated tool; however, it showed slower rate of tool wear indicating better tool life and the possibility of achieving higher metal removal rates. Hence, it was concluded that the ta-C coated cutting tool performed better than the standard TiAlN coated tool.
Regulation of beta-cell mass by hormones and growth factors. (2001)

Substantial new information has accumulated on molecular mechanisms of pancreas development, regulation of beta-cell gene expression, and the role of growth factors in the differentiation, growth, and regeneration of beta-cells. The present review focuses on some recent studies on the mechanism of action of cytokines such as growth hormone (GH) and prolactin (PRL) in beta-cell proliferation and gene expression-in particular, the role of signal transducers and activators of transcription (STAT) proteins. The implication of the discovery of suppressors of cytokine signaling (SOCS) proteins for the interaction between stimulatory and inhibitory cytokines, including GH, PRL, leptin, and the proinflammatory cytokines interleukin-1 and interferon-gamma, in beta-cell survival is not yet clear. Recent studies indicate a role of cell adhesion molecules and the delta-like protein preadipocyte factor 1/fetal antigen 1 (Pref-1/FA-1) in cytokine-induced beta-cell growth and development. Surprisingly, glucagon-like peptide-1 (GLP-1) was recently found to stimulate not only insulin secretion but also beta-cell replication and differentiation, which may present a new perspective in treatment of type 2 diabetes. Together with the intriguing reports on positive effects of insulin on both beta-cell growth and function, a picture is emerging of an integrated network of signaling events acting in concert to control beta-cell mass adaptation to insulin demand.
Indirect Electrooxidation of Methane to Methyl Bisulfate on a Boron‐Doped Diamond Electrode (2021)

Abstract Although highly desired and studied for decades, direct methane functionalization to liquid products remains a challenge. We report an electrochemical system using a boron‐doped diamond (BDD) anode in concentrated sulfuric acid that is able to convert methane to methyl bisulfate and methanesulfonic acid without the use of a catalyst by indirect electrochemical oxidation. Due to its high material stability, BDD can be operated at high current densities. High temperature (140 °C) and pressure (70 bar) support the formation of methyl bisulfate to concentrations as high as 160 mM in 3 h and methanesulfonic acid to concentrations of up to 750 mM in 8 h. We present a novel way of catalyst‐free electrochemical methane oxidation and show general trends and limitations of this reaction.
Polarization effects in 4Pi confocal microscopy studied with water-immersion lenses (2000)

We studied the effect of electric field orientation on the point-spread function (PSF) of a 4Pi microscope. We show that in a standard 4Pi arrangement the orientation of the field can be used for changing between constructive- and destructive-mode 4Pi microscopy. The effect is counteracted by introduction of a phase shift of pi into one of the half-arms. This compensation is compulsory during illumination with unpolarized or circularly polarized light. By performing our experiments with 1.2-N.A. water-immersion lenses, we demonstrate that water immersion is suitable for 4Pi confocal microscopy. At a two-photon excitation wavelength of 1064 nm, the water 4Pi confocal PSF features an axial lobe of 40% above and below the focal plane, which, by linear filtering, can be unambiguously removed. The measured axial full width at half-maximum of the PSF is 240 nm. This is 4.3 times narrower than its single-lens confocal counterpart. The 4Pi confocal microscope sets a new resolution benchmark in three-dimensional imaging of watery samples.
[The influence of aging on biological rhythms in human--implications for the pharmacotherapy]. (2006)

This paper rewers to effects of aging on changes in hormonal circadian rhythms. To the most frequent changes related to aging belong attenuation and shortening of amplitude as well as desynchronization of rhythms. These changes may determine pathophysiological and therapeutic base for hormonal therapy.
Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells (2021)

ABSTRACT Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to M UTYH- A ssociated P olyposis (MAP) is incompletely understood. Here, we sequenced normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 5-fold in all individuals, except for one showing a 33-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C&gt;A changes. Different mutation rates and signatures between individuals were likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing. Summary
QoS evaluation for web services in cloud computing (2012)

Cloud computing is emanated as a useful paradigm for building applications with cloud services. Different types of resources can be published as services, and a many benefits are delivered with them. Web service in one type of cloud service, which is commonly used and it renders various benefits to service consumers. To understand these benefits, it is necessary to evaluate the quality of web service and maintain comparatively higher level of its quality based on the evaluation result. In this paper, we propose a model for evaluating quality of web service. We first define key features of web services. And then, we deduce quality attributes from the key features, and define metrics for the quality attributes. To certify our quality model for web services, we perform assessment based on IEEE 1061. A case study is presented to show its applicability.
Influence of amino acid substitutions in the nisin leader peptide on biosynthesis and secretion of nisin by Lactococcus lactis. (1994)

Structural genes for small lanthionine-containing antimicrobial peptides, known as lantibiotics, encode N-terminal leader sequences which are not present in the mature peptide, but are cleaved off at some stage in the maturation process. Leader sequences of the different lantibiotics share a number of identical amino acid residues, but they are clearly different from sec-dependent protein export signal sequences. We studied the role of the leader sequence of the lantibiotic nisin, which is produced and secreted by Lactococcus lactis, by creating site-directed mutations at various positions in the leader peptide sequence. Mutations at Arg-1 and Ala-4, but not at the conserved Pro-2, strongly affected the processing of the leader sequence and resulted in the extracellular accumulation of a biologically inactive precursor peptide. Amino acid analysis and 1H NMR studies indicated that the precursor peptide with an Ala-4-->Asp mutation contained a modified nisin structural part with the (mutated) unmodified leader sequence still attached to it. The Ala-4-->Asp precursor peptide could be activated in vitro by enzymatic cleavage with trypsin, liberating nisin. These results confirmed that cleavage of the leader peptide is the last step in nisin maturation and is necessary to generate a biologically active peptide. Several mutations, i.e. Pro-2-->Gly,Pro-2-->Val, Asp-7-->Ala,Lys-9-->Leu,Ser-10-->Ala/Ser-12-->Ala and Val-11-->Asp/Val-13-->Glu in the leader peptide did not have any detectable effect on nisin production and secretion, although some of them affected highly conserved residues. When mutations were created in the -18 to -15 region of the nisin leader peptide (i.e. Phe-18-->Leu,Leu-16-->Lys,Asp-15-->Ala), no secretion or intracellular accumulation could be detected of nisin or its precursors. This suggested that these conserved residues are involved in the maturation process and may interact with lantibiotic-specific modifying enzymes.
Emerging and future trends in seismic attributes (2008)

Seismic attributes extract information from seismic reflection data that can be used for quantitative and qualitative interpretation. Attributes are used by geologists, geophysicists, and petrophysicists to map features from basin to reservoir scale. Some attributes, such as seismic amplitude, envelope, rms amplitude, spectral magnitude, acoustic impedance, elastic impedance, and AVO are directly sensitive to changes in seismic impedance. Other attributes such as peak-to-trough thickness, peak frequency, and bandwidth are sensitive to layer thicknesses. Both classes of attributes can be quantitatively correlated to well control using multivariate analysis, geostatistics, or neural networks. Seismic attributes such as coherence, Sobel filter-based edge detectors, amplitude gradients, dip-azimuth, curvature, and gray-level co-occurrence matrix measures are directly sensitive to seismic textures and morphology. Geologic models of deposition and structural deformation coupled with seismic stratigraphy principles and seismic geomorphology allow us to qualitatively predict geologic facies.
Insulin resistance in dialysis versus non dialysis end stage renal disease patients without diabetes. (2011)

Impaired insulin sensitivity in both dialysis groups after long term dialysis was still higher than that of the non dialysis ESRD group. However, no significant differences were noted between CAPD and HD treatments.
A Randomized Clinical Trial Evaluating Sequential Methotrexate and Fluorouracil in the Treatment of Patients with Node-Negative Breast Cancer Who Have Estrogen-Receptor-Negative Tumors (1989)

We evaluated the postoperative use of sequential methotrexate and fluorouracil followed by leucovorin in 679 patients with primary breast cancer, histologically negative axillary nodes, and estrogen-receptor-negative (less than 10 fmol) tumors. No survival advantage was observed with this therapy as compared with no postoperative therapy during four years of follow-up (87 percent vs. 86 percent; P = 0.8). However, there was a significant prolongation of disease-free survival among women who received this therapy as compared with those who did not (80 percent vs. 71 percent; P = 0.003). An advantage was observed in both the patients less than or equal to 49 years old and those greater than or equal to 50. At four years, treatment failure was reduced by 24 percent in the younger group and by 50 percent in the older group. The rates of both local and regional and distant metastases were decreased. These benefits, achieved without the use of an alkylating agent, were associated with tolerable side effects. Multivariate analysis testing for potential interactions failed to identify subgroups of patients who did not benefit from the therapy. These results, although promising, do not obviate the need for additional trials to evaluate potentially better regimens of therapy, but they do suggest that sequential methotrexate-fluorouracil should be used in the control arm in such studies. Their use is also justified for the treatment of patients who refuse to participate in clinical trials, provided the patients meet the eligibility criteria of the present study. Since women with tumors too small for conventional analysis of estrogen-receptor and progesterone-receptor concentrations were not included in this study, we do not recommend systemic treatment for them outside of a clinical trial.
Addressing security challenges in industrial augmented reality systems (2017)

In context of Industry 4.0 Augmented Reality (AR) is frequently mentioned as the upcoming interface technology for human-machine communication and collaboration. Many prototypes have already arisen in both the consumer market and in the industrial sector. According to numerous experts it will take only few years until AR will reach the maturity level to be deployed in productive applications. Especially for industrial usage it is required to assess security risks and challenges this new technology implicates. Thereby we focus on plant operators, Original Equipment Manufacturers (OEMs) and component vendors as stakeholders. Starting from several industrial AR use cases and the structure of contemporary AR applications, in this paper we identify security assets worthy of protection and derive the corresponding security goals. Afterwards we elaborate the threats industrial AR applications are exposed to and develop an edge computing architecture for future AR applications which encompasses various measures to reduce security risks for our stakeholders.
Mapping the Intricate Reactivity of Nanojars toward Molecules of Varying Acidity and Their Conjugate Bases Leading To Exchange of Pyrazolate Ligands (2017)

A comprehensive reactivity study of nanojars toward 18 different acidic compounds with varying pK<sub>a</sub>, including 12 different carboxylic acids (both aliphatic and aromatic mono- and dicarboxylic acids), p-toluenesulfonic acid, hydrogen sulfate, hydrogen carbonate, carbonic acid, 1-decanethiol, and methanol, as well as four different conjugate bases (formate, acetate, benzoate, 2-bromoethanesulfonate) is carried out with the aid of electrospray-ionization mass spectrometry. Thus, the effect on nanojar substitution and breakdown pattern of a number of variables, such as concentration of reagent (acid or conjugate base), acidity of reagent (pK<sub>a</sub>), effect of acid vs conjugate base, steric effects, aromaticity, incarcerated anion and size of the nanojar, is evaluated. Of the substitution and breakdown products identified by mass spectrometry, acetate-substituted nanojars (Bu<sub>4</sub>N)<sub>2</sub>[CO<sub>3</sub>⊂{Cu<sub>27</sub>(μ-OH)<sub>27</sub>(μ-pz)<sub>27-x</sub>(μ-CH<sub>3</sub>COO)<sub>x</sub>}] (x = 1 and 2), as well as dimeric complexes (Bu<sub>4</sub>N)<sub>2</sub>[Cu<sub>2</sub>(μ-pz)<sub>2</sub>A<sub>2</sub>] (A = CO<sub>3</sub><sup>2-</sup> and SO<sub>4</sub><sup>2-</sup>) have been isolated and characterized by single-crystal X-ray diffraction. This study offers a detailed understanding of the behavior of nanojars of various sizes and with different incarcerated anions in the presence of the above-mentioned compounds at varying concentrations and tests the limits of the pyrazolate/carboxylate structural analogy in multinuclear metal complexes. The results point to the possibility of obtaining functionalized nanojars via pyrazolate/carboxylate ligand exchange, an aid in the design of anion extraction processes using nanojars or similar complexes as extracting agents.
Abstract 135: Correlation of TICI Reperfusion with MR Reperfusion, Infarct Growth and Clinical Outcome in the DEFUSE 2 Trial (2012)

Background: The Thrombolysis In Cerebral Infarction (TICI) score is a widely used angiographic score in endovascular stroke studies. Assessment of reperfusion based on perfusion weighted MRI (PWI reperfusion) has been used more commonly in patients treated with intravenous thrombolysis. This analysis of the DEFUSE 2 study data was undertaken to 1) determine the association between TICI and PWI reperfusion and 2) assess the association between TICI-reperfusion and clinical and radiographic outcomes. Methods: Patients undergoing acute endovascular stroke therapy of anterior circulation strokes were enrolled in a prospective multi-center study (DEFUSE 2) if an MRI could be obtained within 90 minutes before endovascular treatment and repeated within 12 hours after the intervention. Only patients with a TICI score of 0 or 1 on baseline digital subtraction angiography (DSA) were included in this analysis. A single blinded reader at the core imaging facility determined pre- and post-procedure TICI scores. TICI-reperfusion was defined as a TICI score of 2B or 3. PWI lesion volumes were assessed using fully automated software (RAPID). PWI-reperfusion was defined as a reduction in PWI(Tmax&gt;6s) lesion volume of &gt;50% between baseline and early follow-up. Infarct growth was defined as the difference between baseline DWI and 5-day FLAIR lesion volume. Favorable clinical response was defined as a NIHSS score of 0-1 at day 30 or an improvement in NIHSS score of ≥8 points between baseline and day 30. Results: This preliminary analysis includes 68 of 101 patients who underwent endovascular therapy and had adequate PWI data to assess reperfusion (final results will be presented at the meeting). At completion of endovascular treatment 30% of the patients remained TICI 0 or 1, 27% improved to TICI 2A, 29% to TICI 2B, and 13% had complete reperfusion (TICI 3). Better TICI-reperfusion scores were associated with higher rates of reperfusion assessed by PWI. PWI-reperfusion was seen in 32% of patients who remained TICI 0-1, 53% with TICI 2A, 98% with TICI 2B, and 100% with TICI 3 reperfusion. Agreement between TICI-reperfusion and PWI-reperfusion was moderate (kappa 0.51). The incidence of favorable clinical response increased with higher TICI scores: 35% with TICI 0-1, 44% with TICI 2A, 72% with TICI 2B, and 67% with TICI 3. Patients who met pre-specified DEFUSE 2 criteria for reperfusion (TICI 2B/3) were more likely to have a favorable clinical response (70% vs 40%; p=0.015), and had less median [IQR] lesion growth (10 [2-56] ml vs 67 [28-122] ml; p=0.001) than patients without TICI-reperfusion. Conclusion: TICI 2B or 3 reperfusion following endovascular therapy for acute anterior circulation stroke is highly correlated with PWI reperfusion. Patients with TICI 2B or 3 reperfusion show less infarct growth and are more likely to have a favorable clinical response.