gebhart/patrepeval huggingface dataset:
Genetic compensation for sarcoglycan loss by integrin α7β1 in muscle (2004)

Disruption of the sarcoglycan complex leads to muscle membrane instability and muscular dystrophy in humans and mice. Through the dystrophin glycoprotein complex, sarcoglycan participates in connecting the internal cytoskeleton to the membrane and the extracellular matrix. Integrin alpha7beta1 is also a transmembrane protein of skeletal and cardiac muscle that similarly links the cytoskeleton to the extracellular matrix. Mice lacking integrin alpha7 develop mild muscle degeneration, while sarcoglycan mutant mice display overt muscle degeneration and muscular dystrophy. In sarcoglycan-deficient muscle, integrin alpha7 protein was upregulated at the plasma membrane. To ascertain whether integrin alpha7 upregulation compensates for the loss of the transmembrane sarcoglycan linkage in sarcoglycan-deficient muscle, we generated mice lacking both integrin alpha7 and gamma-sarcoglycan (gxi). These double-mutant gxi mice exhibit profound, rapid muscle degeneration leading to death before one month of age consistent with a weakened cellular attachment to the extracellular matrix. The regenerative capacity of gxi muscle was intact with increased embryonic myosin heavy chain expression, myofiber central nucleation and normal in vivo myoblast differentiation. Therefore, upregulation of integrin alpha7beta1 compensates as a transmembrane muscle cell attachment for sarcoglycan consistent with overlapping roles for sarcoglycan and integrins in mediating cytoskeletal-membrane-extracellular matrix interaction.
Anti-Tumor Activity of the Aurora a Inhibitor MLN8237 in Diffuse Large B-Cell Lymphoma Preclinical Models. (2008)

Abstract Aurora A kinase is a serine/threonine protein kinase that is essential for normal transit of cells through mitosis. In many tumor types the Aurora A gene is amplified and/or the protein is over-expressed. The Aurora A small-molecule inhibitor MLN8237 demonstrated robust tumor growth inhibition in xenograft models of solid tumors grown subcutaneously (S.C.) in immunocompromised mice. Here we explored the antitumor activity of MLN8237 in models of diffuse large B-cell lymphoma (DLBCL) both in vitro and in vivo. In vivo three established DLBCL xenograft models (OCI-Ly7, OCI-Ly19, and WSU-DLCL2; all cells expressing luciferase) and a primary DLBCL tumor model PHTX-22-06 were tested using MLN8237 at different doses. Rituximab, an anti-CD20 monoclonal antibody that is active against CD20+ malignant B cells and is a standard of care agent was used for comparison. Using these model systems, tumor cells were injected either I.V. (to evaluate disseminated disease), or S.C. in severe combined immunodeficient mice (SCID). Animals were dosed orally for 21 days with MLN8237 (QD or BID) at various doses, or Rituximab dosed at 10mg/kg IV (once/week) and tumor growth inhibition was monitored using either bioluminescent imaging for the disseminated models or vernier calipers for the S.C. models. Tumor growth inhibition by MLN8237 was dose dependent with 20 mg/kg bid being the most efficacious dose (TGI&amp;gt;100% in both disseminated OCI-Ly19 and WSU models). All animals in the OCI-Ly19 disseminated model 20 mg/kg BID treatment group demonstrated regressions and remained disease free until the end of the study, day 65. In this study the Rituximab treated animals were euthanized on day 31 due to a high level of tumor burden. In the primary tumor model, PHTX-22-06, MLN8237 dosed at 20 mg/kg BID was also the most efficacious with a TGI of 95%. Moreover, tumor growth inhibition was durable as determined by prolonged tumor growth delay (&amp;gt;50 days). Significant efficacy was achieved in all models tested, whether grown as disseminated or subcutaneous models. A noted increase in durability of response was observed with MLN8237 treatment when compared with previous data from solid tumor models. In vitro, MLN8237 treatment increased levels of apoptosis in the OCI-Ly19 cells in comparison to the solid tumor cell line HCT-116 (colon). Greater Annexin V positive cells and greater cleaved PARP and Caspase-3 signals were detected in the MLN8237 treated OCI-Ly19 cells when compared to HCT-116 cells. The demonstration of robust and durable anti-tumor activity in preclinical models treated with MLN8237 provides the basis for its clinical evaluation as a treatment option for DLBCL. MLN8237 is currently in multiple Phase I clinical trials.
Immunogenicity Evaluation of N-Glycans Recognized by HIV Broadly Neutralizing Antibodies (2021)

While the improved treatment of human immunodeficiency virus type 1 (HIV-1) infection is available, the development of an effective and safe prophylactic vaccine against HIV-1 is still an unrealized goal. Encouragingly, the discovery of broadly neutralizing antibodies (bNAbs) from HIV-1 positive patients that are capable of neutralizing a broad spectrum of HIV-1 isolates of various clades has accelerated the progress of vaccine development in the past few years. Some of these bNAbs recognize the N-glycans on the viral surface gp120 glycoprotein. We have been interested in using the glycan epitopes recognized by bNAbs for the development of vaccines to elicit bNAb-like antibodies with broadly neutralizing activities. Toward this goal, we have identified novel hybrid-type structures with subnanomolar avidity toward several bNAbs including PG16, PGT121, PGT128-3C, 2G12, VRC13, VRC-PG05, VRC26.25, VRC26.09, PGDM1400, 35O22, and 10-1074. Here, we report the immunogenicity evaluation of a novel hybrid glycan conjugated to carrier DT<sub>CRM197</sub>, a nontoxic mutant of the diphtheria toxin, for immunization in mice. Our results indicated that the IgG response was mainly against the chitobiose motif with nonspecific binding to a panel of N-glycans with reducing end GlcNAc-GlcNAc (chitobiose) printed on the glass slides. However, the IgM response was mainly toward the reducing end GlcNAc moiety. We further used the glycoconjugates of Man<sub>3</sub>GlcNAc<sub>2</sub>, Man<sub>5</sub>GlcNAc<sub>2</sub>, and Man<sub>9</sub>GlcNAc<sub>2</sub> glycans for immunization, and a similar specificity pattern was observed. These findings suggest that the immunogenicity of chitobiose may interfere with the outcome of N-glycan-based vaccines, and modification may be necessary to increase the immunogenicity of the entire N-glycan epitope.
A Wireless Fingerpring Attendance System (2016)

In this paper we design a system which takes student attendance and the attendance records are maintained automatically in an academic institute. Taking the attendance manually and maintaining its record till end of year (or even beyond) is very difficult job as well as wastage of time and paper. This necessitates an efficient system that would be fully automatic. Top level design of the system includes marking attendance with the help of a finger-print sensor module and saving the records to a computer or server. Fingerprint sensor module and LCD screen are portable although they can also be fixed to a location for e.g. entry/ exit points. To begin with, a student needs to be registered in the finger-print sensor module. Thereafter every time the student attends a lecture he/ she will place his/her finger on the fingerprint sensor module. The finger-print sensor module will update the attendance record in database. The student can see the notification on LCD screen.
Understanding Fuzzy Logic: An Interview with Lotf i Zadeh [DSP History] (2007)

This paper presents the interview of Lotfi Zadeh. He share his views through fuzzy logic glasses.
A New Mobile Robot Guidance System Using Optical Reflectors (2005)

We present a new guidance system using optical reflectors as landmarks. The advantages of using the reflectors are; (1) easy to identify, (2) inexpensive, (3) easy to set up, and (4) inconspicuous to human. We also present a method to generate and follow smooth paths between the discrete landmarks, and to control a mobile robot in real-time for a smooth and non-stop motion.
A Versatile Approach for Functionalization of 3-Aryl-3-trifluoromethyldiazirine Photophor (1997)

We introduce here a novel and simple method for the carbonylation of (alkoxypheny1)diazirine.3-(3-Methoxypheny1)-3-trifluoromethyldiazirine was found to be stable under a typical Friedel-Crafts reaction producing carboxaldehyde derivatives of methoxyphenyldiazirine. l 3 e formyl group was easily converted to carboxylic acid, olefin, alcohol, or benzyl bromide providing new derivatives of diazirine photophor in the field of photoaffinity labeling.The technique of photoaffinity labeling has become increasingly appreciated as a powerful chemical methodology for the detailed strnctural analysis.of ligand binding domains. 1Although 3-aryl-3trifluoromethyldiazirines appear to come closest to satisfying the chemical and biological criteria required for
TRAIL‐Induced Caspase Activation Is a Prerequisite for Activation of the Endoplasmic Reticulum Stress‐Induced Signal Transduction Pathways (2015)

It is well known that tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis can be initially triggered by surface death receptors (the extrinsic pathway) and subsequently amplified through mitochondrial dysfunction (the intrinsic pathway). However, little is known about signaling pathways activated by the TRAIL-induced endoplasmic reticulum (ER) stress response. In this study, we report that TRAIL-induced apoptosis is associated with the endoplasmic reticulum (ER) stress response. Human colorectal carcinoma HCT116 cells were treated with TRAIL and the ER stress-induced signal transduction pathway was investigated. During TRAIL treatment, expression of ER stress marker genes, in particular the BiP (binding immunoglobulin protein) gene, was increased and activation of the PERK (PKR-like ER kinase)-eIF2α (eukaryotic initiation factor 2α)-ATF4 (activating transcription factor 4)-CHOP (CCAAT-enhancer-binding protein homologous protein) apoptotic signal transduction pathway occurred. Experimental data from use of a siRNA (small interfering RNA) technique, caspase inhibitor, and caspase-3-deficient cell line revealed that TRAIL-induced caspase activation is a prerequisite for the TRAIL-induced ER stress response. TRAIL-induced ER stress was triggered by caspase-8-mediated cleavage of BAP31 (B cell receptor-associated protein 31). The involvement of the proapoptotic PERK-CHOP pathway in TRAIL-induced apoptosis was verified by using a PERK knockout (PERK(-/-)) mouse embryo fibroblast (MEF) cell line and a CHOP(-/-) MEF cell line. These results suggest that TRAIL-induced the activation of ER stress response plays a role in TRAIL-induced apoptotic death.
Coupling Performance Enhancement of GaSb-Based Single-Transverse-Mode Lasers with Reduced Beam Divergence Obtained via near Field Modulation (2022)

Symmetric narrow waveguide structure has been developed and fabricated to achieve low beam divergence and improved coupling performance of the 1.95 μm GaSb-based single-transverse-mode diode lasers. The near-field expansion effect of the narrowed 150 nm vertical waveguide design leads to a reduced fast-axis beam divergence of 44.2° full width at half maximum (FWHM) as well as 62% single-mode fiber (SMF) coupling efficiency, which has 55% relative promotion compared to the 40% efficiency of the conventional 270 nm waveguide design with 60.4° FWHM. The highest SMF coupling power of 113 mW was obtained by the 210 nm narrow waveguide lasers with lower internal optical loss at a 55% coupling efficiency, which performed balanced optimal performance with a narrowed divergence of 53.4° and a relatively high optical power of 206 mW. The high coupling efficiency and power will provide more promising prospects for the GaSb-based single-transverse-mode lasers in the widespread fiber-based and external-cavity applications.
Teacher Education and Multiple Intelligences: A Case Study of Multiple Intelligences and Teacher Efficacy in Two Teacher Preparation Courses (2004)

This instrumental collective case study provides an in-depth description of the change that transpired in two multiple intelligence (MI)–based graduate-level teacher preparation courses. Qualitative and quantitative data were collected and analyzed. Implications for MI in teacher education are discussed.
Software Accuracy-Based Sensor Network Design and Upgrade in Process Plants (2010)

In this paper we present a new method for linear and nonlinear sensor network design with applications to variable estimation based on the use of accuracy and residual accuracy. Accuracy has been shown recently to be a better substitute for existing data-reconciliation network properties, such as precision, residual precision, gross error detectability and resilience as pointed out in our previous works (the first two references). We explore the numerical difficulties associated to different ways of calculating accuracy and different methods used to optimize the cost.
A WOS/sup TM/-based solution for high performance computing (2002)

Most of the development environments for high performance parallel applications require that all the computing modules and resources be known in advance. The execution environment must know where the different program modules will be executed, and must properly configure each computer involved in the execution. We describe how the Web Operating System (WOS/sup TM/) environment may be used to dynamically adjust the granularity of parallel programs, locate available computers to perform the computations and how these computers are dynamically configured. The WOS (P. Kropf et al., 2000) is a metacomputing environment suitable for supporting and managing distributed parallel processing on wide and local networks. Communication between WOS nodes is realized through a generic service protocol (WOSP) and a discovery/location protocol (WOSRP). WOSP may be versioned to support specialized services. The authors focus on the design of two such versions for parallel/distributed applications and high performance computing. These versions support the location and setup of computational nodes for these applications.
Simulating geomagnetic bird navigation using novel high-resolution geomagnetic data (2022)

Birds rely on precise navigational mechanisms, especially for long-distance migrations. One debated mechanism is their use of the geomagnetic field. It is unclear if and how different species of birds are using intensity or inclination (or both) for navigation. Previous geomagnetic modelling research is based on static geomagnetic data despite a temporally and spatially varying geomagnetic field. Animals supposedly have a high sensitivity to those changes of the geomagnetic field. In order to understand how birds respond in real-time to its temporal variation, we need to use accurate geomagnetic information linked to the position of the bird through co-location in space and time. We developed a data-driven approach to simulate geomagnetic migratory strategies, using, for the first time, accurate contemporaneous geomagnetic data obtained from Swarm satellites of the European Space Agency. We created biased correlated random walk models which were based on both GPS data from greater white-fronted geese (Anser albifrons) during fall migration between north-west Russia and central Europe and contemporaneous satellite geomagnetic data. Different strategies of geomagnetic navigation associated with different geomagnetic values were translated into probability surfaces, built from geomagnetic data, and included into the random walk models. To evaluate which strategy was most likely, we compared the measured GPS trajectories to the simulated trajectories using different trajectory similarity measurements. We propose this as an approach to track many bird species for future comparative studies. We found that navigational strategies in these geese using magnetic intensity were closer to the observed data than those using inclination. This was the case in 80% of the best models and is an indication that it should be more beneficial for these geese to use intensity over inclination. Additionally, our results supported results from a previous study, that navigation based on taxis and compass mechanisms were more similar to the observed data than other mechanisms. We therefore suggest that these geese may use a combination of these strategies for navigation at a broad-scale. Overall, it seems likely that for successful navigation to the target location more than one mechanism is necessary; indicating a multifactorial navigation mechanism of these migratory geese in the study area. The satellite geomagnetic data are available at a higher temporal resolution and the use significantly improved the fit of the modelled simulations in comparison to the modelled geomagnetic data. Therefore, using annotated geomagnetic data could greatly improve the modelling of animal geomagnetic navigation in future research.
Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry (2019)

Hip geometry is an important predictor of fracture. We performed a meta-analysis of GWAS studies in adults to identify genetic variants that are associated with proximal femur geometry phenotypes. We analyzed four phenotypes: (i) femoral neck length; (ii) neck-shaft angle; (iii) femoral neck width, and (iv) femoral neck section modulus, estimated from DXA scans using algorithms of hip structure analysis. In the Discovery stage, 10 cohort studies were included in the fixed-effect meta-analysis, with up to 18,719 men and women ages 16 to 93 years. Association analyses were performed with ∼2.5 million polymorphisms under an additive model adjusted for age, body mass index, and height. Replication analyses of meta-GWAS significant loci (at adjusted genomewide significance [GWS], threshold p ≤ 2.6 × 10<sup>-8</sup> ) were performed in seven additional cohorts in silico. We looked up SNPs associated in our analysis, for association with height, bone mineral density (BMD), and fracture. In meta-analysis (combined Discovery and Replication stages), GWS associations were found at 5p15 (IRX1 and ADAMTS16); 5q35 near FGFR4; at 12p11 (in CCDC91); 11q13 (near LRP5 and PPP6R3 (rs7102273)). Several hip geometry signals overlapped with BMD, including LRP5 (chr. 11). Chr. 11 SNP rs7102273 was associated with any-type fracture (p = 7.5 × 10<sup>-5</sup> ). We used bone transcriptome data and discovered several significant eQTLs, including rs7102273 and PPP6R3 expression (p = 0.0007), and rs6556301 (intergenic, chr.5 near FGFR4) and PDLIM7 expression (p = 0.005). In conclusion, we found associations between several genes and hip geometry measures that explained 12% to 22% of heritability at different sites. The results provide a defined set of genes related to biological pathways relevant to BMD and etiology of bone fragility. © 2019 American Society for Bone and Mineral Research.
Lysogenic conversion of staphylococcal lipase is caused by insertion of the bacteriophage L54a genome into the lipase structural gene (1986)

Staphylococcus aureus PS54 manifests no lipase (geh) activity. This is due to the insertion of bacteriophage L54a DNA into the geh structural gene. The nucleotide sequence of this 2,968-base-pair DNA fragment was determined. Lipase deduced from the nucleotide sequence is a polypeptide of 690 amino acids which extends from nucleotide 706 to 2776.
ChemInform Abstract: Substituent Control in the Synthesis of Azetidines and Pyrrolidines by N‐Tosyloxiraneethylamines Base‐Mediated Cyclization. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Proton stopping measurements at low velocity in warm dense carbon (2022)

Ion stopping in warm dense matter is a process of fundamental importance for the understanding of the properties of dense plasmas, the realization and the interpretation of experiments involving ion-beam-heated warm dense matter samples, and for inertial confinement fusion research. The theoretical description of the ion stopping power in warm dense matter is difficult notably due to electron coupling and degeneracy, and measurements are still largely missing. In particular, the low-velocity stopping range, that features the largest modelling uncertainties, remains virtually unexplored. Here, we report proton energy-loss measurements in warm dense plasma at unprecedented low projectile velocities. Our energy-loss data, combined with a precise target characterization based on plasma-emission measurements using two independent spectroscopy diagnostics, demonstrate a significant deviation of the stopping power from classical models in this regime. In particular, we show that our results are in closest agreement with recent first-principles simulations based on time-dependent density functional theory.
A Novel Mouse Model of Chronic Inflammatory and Overactive Bladder by a Single Intravesical Injection of Hydrogen Peroxide (2013)

There is so far no generally accepted animal model of chronic cystitis by which potential therapies can be evaluated. In this study, we aimed to establish a new mouse model of cystitis based on the proinflammatory effects of reactive oxygen species. A single intravesical injection of 1.5% hydrogen peroxide (H2O2) significantly increased the numbers of voids by 1 day after injection in female mice, which lasted up to 7 days. The H2O2 injection rapidly increased the bladder weight by 3 h in parallel with the histological damage and hyperpermeability of urothelial barrier. Although the urothelial dysfunction was recovered to normal by 7 days, increase in bladder weight, edematous thickening of the submucosa, and vascular hyperpermeability were apparent even 7 days after injection. During the time course, massive infiltration of neutrophils and increased expression of inflammatory cytokines were observed in the bladder. An intraperitoneal administration of oxybutynin, amitriptyline, indomethacin, or morphine attenuated the H2O2-induced frequent urination. These findings suggest that an intravesical injection of H2O2 induces relatively long-lasting inflammatory and overactive bladder, compared with existing cystitis models. The intravesical H2O2 injection model may be a simple and useful tool in the pathological study and drug discovery for chronic cystitis.