gebhart/patrepeval huggingface dataset:
Characterization of BC1-2, BC1-XL, and Bax Pore Formation and Their Role in Apoptosis Regulation (1999)

Abstract : The Bcl-2 protein family plays an important role in governing a cell's decision to live or die. Dysregulation of these proteins is observed in many breast cancer cases and thus it is important to understand their mechanism in order to develop new treatments. The Bcl-X(L) protein structure showed a strong similarity to pore-forming bacterial toxins, suggesting that Bcl-2 protein family protein may regulate apoptosis by pore formation or membrane insertion. Single cysteine mutants of Bcl-X(L) have been generated to probe the topology of the membrane-inserted state. Preliminary results show that the BH3 domain is present on the membrane surface but it is unclear as to whether this portion of the protein is actually membrane-inserted. Labeling of these cysteine mutants with thiol- specific probes such as BODIPY also yielded results suggesting that residues in both the putative pore-forming fifth a-helix and the BH3 domain were still solvent accessible, as indicated by the ability of a fluorescence- quenching anti-BODIPY antibody to quench fluorescence in the presence and absence of lipid vesicles on which the proteins display channel-forming capability.
Design, optimization and manufacturing of a spoke type interior permanent magnet synchronous motor for low voltage-high current servo applications (2013)

This paper talks about some design issues for spoke type interior permanent magnet (IPM) motor for low voltage high current servo applications. After initial motor design, several analyses to improve the motor's torque quality have been carried out using Finite Element Analysis (FEA). Effect of skewing and segmented rotors has also been explored and the goal of improved torque quality has been realized. A prototype IPM motor has been built, tested and experimentally verified.
1-Adamantanethiolate Monolayer Displacement Kinetics Follow a Universal Form (2007)

Alkanethiol molecules in solution displace 1-adamantanethiolate self-assembled monolayers on Au{111}, ultimately leading to complete molecular exchange. Specifically, here, fast insertion of n-dodecanethiolate at defects in the original 1-adamantanethiolate monolayer nucleates an island growth phase, which is followed by slow ordering of the n-dodecanethiolate domains into a denser and more crystalline form. Langmuir-based kinetics, which describe alkanethiolate adsorption on bare Au{111}, fail to model this displacement reaction. Instead, a Johnson-Mehl-Avrami-Kolmogorov model of perimeter-dependent island growth yields good agreement with kinetic data obtained by Fourier transform infrared spectrometry over 100-fold variation in n-dodecanethiol concentration. Rescaling the growth rate at each concentration collapses all the data onto a single universal curve, suggesting that displacement is a scale-free process. The rate of displacement varies as the square-root of the n-dodecanethiol concentration across the 0.01-1.0 mM range studied.
Increased T-cell receptor repertoire diversity to predict better overall survival in gastrointestinal malignancies. (2021)

474 Background: Severe treatment-induced lymphopenia is a poor prognostic factor for multiple solid malignancies. Emerging data suggests that increased TCR repertoire is associated with improved survival. We hypothesized that increased TCR repertoire following severe treatment-induced lymphopenia would be associated with better survival after accounting for known prognostic factors. Methods: Patients within a prospective cohort were retrospectively analyzed for severe (grade 4) lymphopenia during radiotherapy (RT) at a single institution between 2007-2016. Peripheral blood samples were collected weekly. TCR repertoire at 3 time points were evaluated: pre-RT, during or immediately post-RT at absolute lymphocyte count (ALC) nadir, and ~2 months post-RT. Peripheral blood was analyzed via multiparametric flow cytometry. TCR beta sequencing was performed on immunoSEQ platform from Adaptive Biotechnologies. A Gini diversity index reflecting TCR repertoire was calculated as well as percentage change between ALC nadir and ALC 2 months post-RT. Primary endpoint was overall survival (OS). Cox modeling and Kaplan Meier estimates were used for survival analyses. Results: 109 patients were enrolled. 20 patients were evaluable with complete data. Median follow up was 40 months. Primary malignancy was pancreatic adenocarcinoma in 40%, gastric adenocarcinoma in 30%, and cholangiocarcinoma in 30%. Clinical stage was I-II in 29%, III in 50%, and IV in 21%. 80% underwent chemotherapy (CTX) pre-RT and none received CTX post-RT. 80% had concurrent CTX during RT. Median RT dose was 56 Gy. Among those with pathology available (n = 12), 17% had a pathologic complete response (pCR) and 83% had R0 resection. Median ALC at each of the three study timepoints was 1.26 k/ul, 0.32 k/ul, and 1.02 k/ul, respectively. 4 (20%) patients had increased TCR repertoire as defined by the change in Gini diversity index while 16 (80%) had decreased TCR repertoire post-RT. There were no significant differences in baseline characteristics between the two cohorts. On univariable analysis, increased TCR repertoire from ALC nadir to 2 months post-RT significantly correlated with better OS (HR = 0.20 [95% CI 0.04-0.93]; p = 0.041). Other variables including ECOG, stage, RT dose, CTX use, pCR, R0 resection, baseline WBC, and ALC at three study time points did not correlate with OS. Patients with increased vs decreased TCR repertoire post-RT had a 3-year OS of 75% vs 22%, respectively (log rank p = 0.026). Conclusions: Increased TCR repertoire post-RT was an independent prognostic factor for better OS in our cohort of GI malignancies. Our findings provide biologic insight and refine the association between ALC and cancer outcomes. TCR repertoire warrants further study as a predictive and prognostic biomarker in GI malignancies. Therapeutic approaches to limit severe lymphopenia are ongoing and should include TCR assessment.
Alzheimer's amyloid precursor protein produced by recombinant baculovirus expression. Proteolytic processing and protease inhibitory properties. (1991)

The baculovirus expression system was used to generate recombinant Alzheimer's amyloid precursor (AAP) proteins. Recombinant baculoviruses were constructed, designed to express full-length 695-, 751-, and 770-amino acid forms. Recombinant baculoviruses designed for constitutive secretion were engineered by placing a termination codon between the beta-protein domain and cytoplasmic anchor of the full-length forms. Insect cells infected with each of these baculoviruses produced both secreted and cell-associated AAPs. Full-length constructs produced secreted derivatives which were COOH-terminally cleaved within the beta-protein domain at Gln15 or Lys16, essentially identical to previous reports utilizing mammalian cell systems. Rare secreted forms (less than 5%) appeared to extend to Lys28. Secretion constructs produced these same forms, but in different ratios. Most (approximately 60%) terminated at Gln15 or Lys16, while the remainder apparently extended to Lys28. AAPs containing the Kunitz-type serine protease inhibitory domain (AAP-751 and -770) were shown to be active inhibitors. No differences were observed in the inhibitors activities of these two forms. The similarities in AAP processing by insect and mammalian systems, together with the large amounts of recombinant protein produced by baculovirus expression, make this an attractive system for studies of AAP processing and biochemical properties.
Immunogenicity of ad libitum drinking water administration of bovine serum albumin in Leghorn chickens (2004)

Oral administration of protein antigen in solution routinely leads to development of oral tolerance in most mammals but has been reported to be fully immunogenic in chickens. Previous studies, including several performed by our laboratory, have demonstrated that oral administration of discrete amounts of BSA for 6 consecutive days is fully immunogenic. This study was performed to determine immunoresponsiveness to protein antigen administered ad libitum at low levels in drinking water compared with i.p. and oral gavage routes of administration. Seven days following the last oral immunization, serum was assayed for IgG, bile for IgA, and tissue culture supernatant from 3 distinct lower intestinal regions for IgG and IgA in immunized and nonimmunized single-comb White Leghorn chickens. Systemic responses in the serum of experimental birds revealed a greater (P < 0.001) IgG response when BSA was administered via i.p. injection or by drinking water compared with gavage administration or nonimmunized controls. Responses measured in bile revealed that BSA administration in the drinking water resulted in a greater (P < 0.001) secretory IgA response compared with i.p. or gavage administration, and negative control groups. Intestinal antigen specific IgG, but not IgA, was elevated (P < 0.05) in all intestinal areas tested in birds immunized against BSA by drinking water and i.p. routes of administration, compared with other experimental groups. Taken together, the present experiments demonstrate that ad libitum drinking water administration of a protein antigen is as effective as i.p. administration or gavage routes of antigen exposure and potentially describe a novel approach to immunization of commercial poultry with purified protein antigens.
Intestinal Host-Microbe Interactions under Physiological and Pathological Conditions (2010)

The intestinal mucosa is unique in that it can be tolerant to the resident, symbiotic microbiota but remaining, at the same time, responsive to and able to fight pathogens. The close interaction between host-symbiotic microbiota at the mucosal level poses important challenges since microbial breaches through the gut barrier can result in the breakdown of gut homeostasis. In this paper, hosts-integrated components that help to preserve intestinal homeostasis including barrier and immune function are discussed. In addition global alterations of the microbiota that can play a role in the initiation of an exaggerated inflammatory response through an abnormal signaling of the innate and adaptive immune response are briefly described.
Characterization of the magnetic moment distribution in low-concentration solutions of iron oxide nanoparticles by a high-Tc superconducting quantum interference device magnetometer (2015)

We developed a highly sensitive AC/DC magnetometer using a high-temperature superconductor superconducting quantum interference device for the evaluation of magnetic nanoparticles in solutions. Using the developed system, we investigated the distribution of magnetic moments of iron oxide multi-core particles of 100 nm at various iron concentrations that are lower than 96 μg/ml by analyzing the measured magnetization curves. Singular value decomposition and non-regularized non-negative least-squares methods were used during the reconstruction of the distribution. Similar distributions were obtained for all concentrations, and the iron concentration could be determined from the measured magnetization curves. The measured harmonics upon the excitation of AC and DC magnetic fields curves agreed well with the harmonics simulated based on the reconstructed magnetization curves, implying that the magnetization curves of magnetic nanoparticles were successfully obtained as we will show in the article. We compared the magnetization curves between multi-core particles of 100 nm and 130 nm, composed of 12-nm iron oxide nanoparticles. A distinctive magnetic property between the 100 nm and 130 nm particles in low-concentration solutions was successfully characterized. The distribution characteristic of magnetic moments suggests that the net magnetic moment in a multi-core particle is affected by the size of the magnetic cores and their degree of aggregation. Exploration of magnetic properties with high sensitivity can be expected using the developed system.
Inhibition of platelet aggregation in vitro and ex vivo by the new thromboxane antagonist (3R)-3-(4-fluorophenylsulfonamido)-1,2,3,4-tetrahydro-9- carbazolepropanoic acid. (1989)

(3R)-3-(4-Fluorophenylsulfonamido)-1,2,3,4-tetrahydro-9-carbazo lepropanoic acid (Bay u 3405) was tested for inhibition of platelet aggregation in vitro (human platelet rich plasma) and ex vivo (rat). Aggregation induced by collagen, arachidonic acid, thrombin, adenosine diphosphate (ADP, biphasic response), epinephrine and U 46619 was inhibited at minimum effective concentrations of 0.01 to 0.1 micrograms/ml in vitro. Following oral administration to rats the ED50 for the dose-dependent inhibition was 36 micrograms/kg. At a dose of 100 micrograms/kg p.o. significant inhibition was obtained up to 16 h. Bay u 3405 is considered a potential drug for treatment of some cardiovascular disorders.
Spatially Resolved Thermoelectric Effects in Operando Semiconductor-Metal Nanowire Heterostructures (2020)

The thermoelectric properties of a nanoscale germanium segment connected by aluminium nanowires are studied using scanning thermal microscopy. The germanium segment of 168\,nm length features atomically sharp interfaces to the aluminium wires and is surrounded by an Al$_2$O$_3$ shell. The temperature distribution along the self-heated nanowire is measured as a function of the applied electrical current, for both Joule and Peltier effects. An analysis is developed that is able to extract the thermal and thermoelectric properties including thermal conductivity, the thermal boundary resistance to the substrate and the Peltier coefficient from a single measurement. Our investigations demonstrate the potential of quantitative measurements of temperature around self-heated devices and structures down to the scattering length of heat carriers.
Performance of the ATLAS track reconstruction algorithms in dense environments in LHC Run 2 (2017)

With the increase in energy of the Large Hadron Collider to a centre-of-mass energy of 13 [Formula: see text] for Run 2, events with dense environments, such as in the cores of high-energy jets, became a focus for new physics searches as well as measurements of the Standard Model. These environments are characterized by charged-particle separations of the order of the tracking detectors sensor granularity. Basic track quantities are compared between 3.2 fb[Formula: see text] of data collected by the ATLAS experiment and simulation of proton-proton collisions producing high-transverse-momentum jets at a centre-of-mass energy of 13 [Formula: see text]. The impact of charged-particle separations and multiplicities on the track reconstruction performance is discussed. The track reconstruction efficiency in the cores of jets with transverse momenta between 200 and 1600 [Formula: see text] is quantified using a novel, data-driven, method. The method uses the energy loss, [Formula: see text], to identify pixel clusters originating from two charged particles. Of the charged particles creating these clusters, the measured fraction that fail to be reconstructed is [Formula: see text] and [Formula: see text] for jet transverse momenta of 200-400 [Formula: see text] and 1400-1600 [Formula: see text], respectively.
Unclassified renal cell carcinoma: an analysis of 85 cases (2007)

These findings indicate that URCC presents with a higher stage and grade, and even after controlling for the stage and grade differences, predisposes patients to 1.6-1.7 times the mortality of CRCC.
Synchronized HHG based source at FLASH (2020)

We present a VUV beamline installed as pump-probe source at the free-electron laser FLASH. The source is based on high-order harmonic generation driven by femtosec-ond near-infrared laser pulses synchronized with the FEL burst mode.
Corrigendum: Glycotripod Amphiphiles for Solubilization and Stabilization of a Membrane‐Protein Superassembly: Importance of Branching in the Hydrophilic Portion (2013)

The structures in Scheme 1 and the structure of TPA-2-S in the main text and the Table of Contents were inadvertently drawn as l-rather than d-sugars. The correct stereochemistries of the carbohydrates are shown here. The authors apologise for this error.
Military Avionics Fiber Optics Photonics Packaging Technology Forecast (2007)

A new wave of photonics packaging research and development is required to enable a robust next generation BIT-capable avionics LAN technology solution based on single mode fiber and advanced WDM and RF components. Similarly, for high-speed point-to-point multimode fiber-optic links, cost-effective transmitter and receiver (transceiver) packaging with in-package optical BIT capability is needed to enable fully BIT-capable fiber optic links on legacy and future military / aerospace platforms.
TD-PSOLA versus harmonic plus noise model in diphone based speech synthesis (2002)

In an effort to select a speech representation for our next generation concatenative text-to-speech synthesizer, the use of two candidates is investigated; TD-PSOLA and the harmonic plus noise model, HNM. A formal listening test has been conducted and the two candidates have been rated regarding intelligibility, naturalness and pleasantness. Ability for database compression and computational load is also discussed. The results show that HNM consistently outperforms TD-PSOLA in all the above features except for computational load. HNM allows for high-quality speech synthesis without smoothing problems at the segmental boundaries and without buzziness or other oddities observed with TD-PSOLA.
Determination of the complanar geometric lattice parameters of monocrystals with high precision (1985)

Abstract A measuring method is presented which allows to determine the complanar geometric lattice parameters (the amounts of two unit cell vectors and the angle between the both unit cell vectors) of monocrystals with high precision at one crystal point and in one measurement cycle. The efficiency of the method is demonstrated at measurements of two quartz monocrystals.
Adaptive Data Delivery Framework for Financial Time Series Visualization (2005)

Nowadays, financial applications spread over various devices in both e-commerce and m-commerce. One of the major tasks in this kind of application is viewing the historical price movement of a stock for the market players before making any decision. However, due to the divergence of the configurations among different devices and platforms, adaptation is necessary for time series data delivery and visualization. In this paper, an adaptive framework of financial time series delivery and visualization is proposed to achieve this goal. The core system adapts the concept of data point importance and data points reordering for time series representation. The application of the proposed framework on stock price time series delivery and visualization is demonstrated in different devices using Web service.
Low–Dielectric Constant Insulators for Future Integrated Circuits and Packages (2011)

Future integrated circuits and packages will require extraordinary dielectric materials for interconnects to allow transistor advances to be translated into system-level advances. Exceedingly low-permittivity and low-loss materials are required at every level of the electronic system, from chip-level insulators to packages and printed wiring boards. In this review, the requirements and goals for future insulators are discussed followed by a summary of current state-of-the-art materials and technical approaches. Much work needs to be done for insulating materials and structures to meet future needs.
Genome-wide scans using archived neonatal dried blood spot samples (2009)

Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.
Aggressive restenosis after percutaneous intervention in two coronary loci in a patient with human immunodeficiency virus infection (2017)

A 54-year-old black African woman, 22 years human immunodeficiency virus (HIV)-positive, presented with an acute coronary syndrome. She was taking two nucleoside reverse transcriptase inhibitors and two protease inhibitors. Viral load and CD4 count were stable. Angiography revealed a right coronary artery lesion, which was treated with everolimus eluting stent. She also underwent balloon angioplasty to the first diagonal. She re-presented on three different occasions and technically successful coronary intervention was performed. The patient has reported satisfactory compliance with dual anti platelet therapy throughout. She was successfully treated with surgical revascularisation. The patient did not experience any clinical recurrence on follow up. This case demonstrates exceptionally aggressive multifocal and recurrent instent restenosis in a patient treated for HIV infection, raising the possibility of an association with HIV infection or potentially components of retro viral therapy.
An intermediate methylation signature is associated with improved patient survival and a distinct global mRNA expression profile in glioblastoma: An interim analysis of The Cancer Genome Atlas data (2008)

PL04 The Cancer Genome Atlas (TCGA) project is an ongoing study with a goal of describing the variety of molecular aberrations that occur in glioblastoma (GBM) by the use of high-throughput molecular platforms on clinically annotated tumor specimens. One such platform includes methylation of approximately 3,000 CpG islands using the Illumina Golden Gate array. Data were available for 183 GBM patients for an interim analysis. Data were filtered to include the CpG islands that showed high variation among the samples, resulting in 143 CpG islands, which were subject to unsupervised hierarchical clustering. This cluster analysis revealed 3 groups of tumors differing according to the degree of overall methylation. One group exhibited extensive methylation, a second showed very low levels of methylation and a third was defined by hyper-/hypomethylation of specific CpG islands (the intermediate group). The intermediate group was further characterized by methylation of a specific set of genes that were unmethylated in the other groups, and included HRB2 , NETO2 , WNT10B , LAYN and PCDHB2 .  A survival analysis showed that the intermediate group had a significantly improved overall survival (p FABP5 , RBP1 , FAS , THBS1 and ICA1 . Among the 13 genes specifically methylated in the other 2 groups, 3 genes (23%) showed a concordant decrease in expression ( NPY , NEFL and TUSC3 ). Interestingly, the global gene expression profile of the intermediate methylation subgroup greatly differed from the other 2 subgroups. In particular, this group showed increased expression of genes whose over-expression we have previously found to be correlated with improved outcome, including SNAP91 , DCX , RP11-35N6.1 , TUSC3 , and RTN1 , genes associated with neural development. Genes previously associated with poor outcome, including CHI3L1 (YKL-40), PDPN , NNMT , and TIMP1 as well as additional extracellular matrix/mesenchymal genes were under-expressed in this group. In all, there were over 200 genes with a ≥2.5-fold difference in mRNA expression between the intermediate subgroup versus the other 2 groups, but minimal gene expression variability between the high and low methylation groups, respectively.  Taken together, these data suggest that CpG methylation profiles represent a source of robust biomarkers in GBM, are extensively intertwined with the global gene expression profile, and corroborate our previously described concept of a prognostically unfavorable, mesenchymal subgroup and favorable, proneural subgroup. Importantly, it also provides proof-of-concept that the cross-platform analyses made possible by TCGA will lead to new insights regarding the molecular complexity of GBM.