gebhart/patrepeval huggingface dataset:
Targeted Resequencing of the Pericentromere of Chromosome 2 Linked to Constitutional Delay of Growth and Puberty (2015)

Constitutional delay of growth and puberty (CDGP) is the most common cause of pubertal delay. CDGP is defined as the proportion of the normal population who experience pubertal onset at least 2 SD later than the population mean, representing 2.3% of all adolescents. While adolescents with CDGP spontaneously enter puberty, they are at risk for short stature, decreased bone mineral density, and psychosocial problems. Genetic factors contribute heavily to the timing of puberty, but the vast majority of CDGP cases remain biologically unexplained, and there is no definitive test to distinguish CDGP from pathological absence of puberty during adolescence. Recently, we published a study identifying significant linkage between a locus at the pericentromeric region of chromosome 2 (chr 2) and CDGP in Finnish families. To investigate this region for causal variation, we sequenced chr 2 between the genomic coordinates of 79-124 Mb (genome build GRCh37) in the proband and affected parent of the 13 families contributing most to this linkage signal. One gene, DNAH6, harbored 6 protein-altering low-frequency variants (< 6% in the Finnish population) in 10 of the CDGP probands. We sequenced an additional 135 unrelated Finnish CDGP subjects and utilized the unique Sequencing Initiative Suomi (SISu) population reference exome set to show that while 5 of these variants were present in the CDGP set, they were also present in the Finnish population at similar frequencies. Additional variants in the targeted region could not be prioritized for follow-up, possibly due to gaps in sequencing coverage or lack of functional knowledge of non-genic genomic regions. Thus, despite having a well-characterized sample collection from a genetically homogeneous population with a large population-based reference sequence dataset, we were unable to pinpoint variation in the linked region predisposing delayed puberty. This study highlights the difficulties of detecting genetic variants under linkage regions for complex traits and suggests that advancements in annotation of gene function and regulatory regions of the genome will be critical for solving the genetic background of complex phenotypes like CDGP.
Amplitude Analysis of the Decay (B)over-bar(0) -> K-S(0)pi(+)pi(-) and First Observation of the CP Asymmetry in (B)over-bar(0) -> K* (892)(-)pi(+) (2018)

The time-integrated untagged Dalitz plot of the three-body hadronic charmless decay (B) over bar (0 )-&gt; K-S(0)pi(+)pi(- ) is studied using a pp collision data sample recorded with the LHCb detector, corresponding to an integrated luminosity of 3.0 fb(-1). The decay amplitude is described with an isobar model. Relative contributions of the isobar amplitudes to the (B) over bar (0 )-&gt; K-S(0)pi(+)pi(- ) decay branching fraction and CP asymmetries of the flavor-specific amplitudes are measured. The CP asymmetry between the conjugate (B) over bar (0 )-&gt; K* (892)(-)pi(+) and (B) over bar (0 )-&gt; K* (892)(-)pi(+) decay rates is determined to be -0.308 +/- 0.062.
Enhanced light-extraction from InGaN quantum wells using refractive-index-matched TiO<inf>2</inf> (2007)

Enhancement of the overall luminescence efficiency in InGaN quantum wells by increasing the light-extraction efficiency is demonstrated by lateral patterning of refractive-index- matched TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> films on InGaN quantum well samples.
The covalent structure of bovine liver rhodanese. NH2-terminal sequence and partial structural analysis of tryptic peptides from the citraconylated protein. (1978)

Nineteen tryptic peptides produced by cleavage at 18 of the 20 arginyl residues in citraconylated S-carboxymethylcysteinyl-rhodanese have been isolated by a combination of gel filtration and high voltage paper electrophoresis. These Tc fragments account for all of the 293 residues in the parent polypeptide and their partial or complete sequences have been determined by automated and manual Edman degradation. In some cases, sequence analyses were completed by degradation of peptides derived by secondary cleavages of the decitraconylated Tc fragments with trypsin, chymotrypsin, or the protease from Staphylococcus aureus. Automated Edman degradation of intact S-carboxymethylcysteinyl-rhodanese was performed for 60 cycles; the information thus obtained permitted the alignment of seven of the Tc fragments and gave the sequence of the first 79 residues in the polypeptide chain. The Tc peptide at the COOH terminus of rhodanese was placed by virtue of the fact that it contained no arginine. Structural analysis of the Tc peptides provided the sequences surrounding all five of the methionyl residues in the enzyme. One of the methionines was found in a 19-residue Tc fragment which also contained the cysteinyl residue essential for catalysis.
Influence of exciton lifetime on charge carrier dynamics in an organic heterostructure (2013)

Interactions between charge carriers and excitons, as well as between excitons and optical cavity modes in organic optoelectronic devices are fundamental to their operational limits and chief in preventing the realization of certain phenomena, such as electrically pumped organic lasing. We uncovered a previously unreported phenomenon, wherein optical cavity-modulated exciton decay rate leads to a concomitant modulation in the electrical current of an archetypal NPD/Alq3 organic light emitting device operated in forward bias. The magnitude of this variation is sensitive to the local dielectric environment of the device and is found to be as large as 15%.
The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M β-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation (2017)

CTX-M β-lactamases provide resistance against the β-lactam antibiotic, cefotaxime, but not a related antibiotic, ceftazidime. β-Lactamases that carry the P167S substitution, however, provide ceftazidime resistance. In this study, CTX-M-14 was used as a model to study the structural changes caused by the P167S mutation that accelerate ceftazidime turnover. X-ray crystallography was used to determine the structures of the P167S apoenzyme along with the structures of the S70G/P167S, E166A/P167S, and E166A mutant enzymes complexed with ceftazidime as well as the E166A/P167S apoenzyme. The S70G and E166A mutations allow capture of the enzyme-substrate complex and the acylated form of ceftazidime, respectively. The results showed a large conformational change in the Ω-loop of the ceftazidime acyl-enzyme complex of the P167S mutant but not in the enzyme-substrate complex, suggesting the change occurs upon acylation. The change results in a larger active site that prevents steric clash between the aminothiazole ring of ceftazidime and the Asn170 residue in the Ω-loop, allowing accommodation of ceftazidime for hydrolysis. In addition, the conformational change was not observed in the E166A/P167S apoenzyme, suggesting the presence of acylated ceftazidime influences the conformational change. Finally, the E166A acyl-enzyme structure with ceftazidime did not exhibit the altered conformation, indicating the P167S substitution is required for the change. Taken together, the results reveal that the P167S substitution and the presence of acylated ceftazidime both drive the structure toward a conformational change in the Ω-loop and that in CTX-M P167S enzymes found in drug-resistant bacteria this will lead to an increased level of ceftazidime hydrolysis.
Steps Toward Automated Deprocessing of Integrated Circuits (2017)

Abstract This paper discusses the development of an extensible programmatic workflow that leverages evolving technologies in 2D/3D imaging, distributed instrument control, image processing, and automated mechanical/chemical deprocessing technology. Initial studies involve automated backside mechanical ultra-thinning of 65nm node IC processor chips in combination with SEM imaging and X-ray tomography. Areas as large as 800μm x 800μm were deprocessed using gas-assisted plasma FIB delayering. Ongoing work involves enhancing the workflow with “intelligent automation” by bridging FIB-SEM instrument control and near real-time data analysis to establish a computationally guided microscopy suite.
Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency (2019)

HIV-infected cell lines differ from each other and from cells from ART-treated individuals in the mechanisms governing latent HIV infection. These differences in viral and cellular gene expression must be considered when gauging the suitability of a given cell line for future research on HIV. At the same time, some features were shared across cell lines, such as low expression of antiviral defense genes and a relationship between productive infection and genes involved in survival. These features may contribute to HIV latency or persistence in vivo, and deserve further study using novel single cell assays such as those described in this manuscript.
A case study of a formalized security architecture (2012)

CVS is a widely known version management system, which can be used for the distributed development of software as well as its distribution from a central database. In this paper, we provide an outline of a formal security analysis of a CVS-Server architecture performed in [1]. The analysis is based on an abstract architecture (enforcing a role-based access control on the repository), which is rened to an implementation architecture (based on the usual discretionary access control provided by the POSIX environment). Both architectures serve as framework to formulate access control and condentiality properties. Both the abstract as well as the concrete architecture are specied in the language Z. Based on a logical embedding of Z into Isabelle/HOL, we provide formal, machinechecked proofs for consistency properties of the specication, for the correctness of the renement, and for some security properties. Thus, we present a case study for the security analysis of realistic models over an o-the-shelf system by formal machine-checked proofs.
Evolutionary time series segmentation for stock data mining (2003)

Stock data in the form of multiple time series are difficult to process, analyze and mine. However, when they can be transformed into meaningful symbols like technical patterns, it becomes easier. Most recent work on time series queries concentrates only on how to identify a given pattern from a time series. Researchers do not consider the problem of identifying a suitable set of time points for segmenting the time series in accordance with a given set of pattern templates (e.g., a set of technical patterns for stock analysis). On the other hand, using fixed length segmentation is a primitive approach to this problem; hence, a dynamic approach (with high controllability) is preferred so that the time series can be segmented flexibly and effectively according to the needs of users and applications. In view of the fact that such a segmentation problem is an optimization problem and evolutionary computation is an appropriate tool to solve it, we propose an evolutionary time series segmentation algorithm. This approach allows a sizeable set of stock patterns to be generated for mining or query. In addition, defining the similarity between time series (or time series segments) is of fundamental importance in fitness computation. By identifying perceptually important points directly from the time domain, time series segments and templates of different lengths can be compared and intuitive pattern matching can be carried out in an effective and efficient manner. Encouraging experimental results are reported from tests that segment the time series of selected Hong Kong stocks.
Structured deferral (2013)

We simply do not have a synchronization mechanism that can enforce mutual exclusion.
Some Baeyer–Villiger oxidations using a monooxygenase enzyme from Pseudomonas putida NCIMB 10007 (1993)

G. Grogan, S. M. Roberts and A. J. Willetts, J. Chem. Soc., Chem. Commun., 1993, 699 DOI: 10.1039/C39930000699
Inspiration of the Management of the Private Nankai University to Private Universities (2011)

Private Nankai University is a model of the history of private colleges and universities in China.To research the experiences with its characteristics in education and to analyze the successful process of the development should give some inspiration to the embarrassment of the private universities in the present China.These experiences are valuable proved in practice: they are developing step by step and laying a solid foundation,advancing educational philosophy and the school policy with the times,raising operational funds through multi-channels and effective asset management and stress on teaching quality and improving teaching staff.
Effect of Rare Earth Element Substitution for Vandium on Structure and Electrochemical Characteristic of Ti_(0.26)Zr_(0.07)V_(0.24)Mn_(0.1)Ni_(0.33)Hydrogen Storage Alloys (2014)

Microstructure and electrochemical properties of Ti0.26Zr0.07V0.24-xMn0.1Ni0.33REx(x=0.005, RE=Ce, Nd, Ho,Y) hydrogen storage electrode alloys have been investigated systematically. The results of X-ray diffraction(XRD)show that the matrix phase structure of the alloys are composed of V-based solid solution phase with body centered cubic(bcc) structure and a continuous C14 Laves phase with hexagonal structure. The cell volumes of the two phases are both increase by rare earth elements substitution. The partial substitution of V by rare earth elements can almost improve the activation characteristics and maximum discharge capacity. Lanthanum and neodymium substitution can enhance the maximum discharge capacity of the alloy electrodes observably, and cerium can improve the cyclic stability. Cerium, neodymium, holmium, yttrium can all improve the high-rate ability(HRD) of the alloy electrodes. The alloy electrodes under the condition of high temperature show a favourable discharge performance, and the maximum value of the discharge capacity for the alloy electrodes with neodymium substitution is 550.4 mAh·g-1. The effect on charge retention ability is different with the different rare-earth elements substitutions.
The IBM 2004 Conversational Telephony System for Rich Transcription (2006)

This paper describes the technical advances in IBM's conversational telephony submission to the DARPA-sponsored 2004 rich transcription evaluation (RT-04). These advances include a system architecture based on cross-adaptation; a new form of feature-based MPE training; the use of a full-scale discriminatively trained full covariance Gaussian system; the use of septaphone cross-word acoustic context in static decoding graphs; and the incorporation of 2100 hours of training data in every system component. These advances reduced the error rate by approximately 21% relative, on the 2003 test set, over the best-performing system in last year's evaluation, and produced the best results on the RT-04 current and progress CTS data.
Blockade of Vascular Endothelial Growth Factor (VEGF) Enhances the Therapeutic Efficacy of GM-CSF Secreting Tumor Cell Vaccines (2005)

s: Abstracts for the 20th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer (Primary Authors are Italicized): CELLULAR THERAPIES FOR SOLID AND LIQUID TUMORS
Supplemental Table 4 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Supplemental Table 4&lt;/p&gt;
Expression of the human Bcl-2 increases resistance of Ewing's sarcoma cells to apoptosis and inhibits poly(ADP-ribose) polymerase cleavage induced by radiation (1996)

We reported previously that Ewing's sarcoma (ES) cells respond to ionizing radiation exposure by arrest in G(2)/M phase and induction of apoptosis which occurs in conjunction with poly(ADP-ribose) polymerase (PARP) proteolytic cleavage. ES cells (A4573 cell line) do not express immunodetectable levels of Bcl-2. To determine if expression of Bcl-2 could modulate radiation-induced ES cell death, we have stably transfected A4573 cells with a full-length human bcl-2 cDNA. Expression of Bcl-2 protein rendered ES cells relatively resistant to radiation-induced apoptosis. Moreover, the anti-apoptotic activity of Bcl-2 was directly related to levels of its expression in different ES clones. Cell cycle characteristics were similar for both parental and Bcl-2 expressing ES cells following radiation treatment, although bcl-2 transfectants exhibited a more protracted G(2)/M phase arrest and lower rate of apoptosis after release from the block. Constitutive expression of Bcl-2 resulted in about two-fold inhibition of PARR cleavage in ES cells dying after ionizing radiation exposure. These data support a role for Bcl-2 protein as a negative regulatory element of PARP proteolysis at the early stages of radiation-induced apoptosis in ES cells.
Proteomic profiling of yeast‐ and hyphal‐specific responses ofCandida albicansto the antifungal agent, HWY‐289 (2009)

Virulence of Candida albicans is attributable to its unique dimorphic transition from nonpathogenic yeast cells to pathogenic hyphal cells. We previously discovered a novel antifungal agent, known as HWY-289. To characterize the mechanism underlying HWY-289 antifungal activity, we performed 2-DE to identify proteins that were differentially expressed during yeast-to-hyphal transition and in response to HWY-289. Twenty-four differentially expressed protein spots were identified in HWY-289-treated yeast. Most differentially expressed proteins were involved in carbohydrate-derived energy metabolism, cellular detoxification, and antioxidant defenses. Two proteins were involved in cell cycle regulation and DNA processing, and both were downregulated by HWY-289, suggesting that this agent might promote cell death by weakening cellular defense systems. HWY-289 inhibited yeast-to-hyphal transition in a dose-dependent manner. 2-DE analysis of hyphae uncovered several proteins that were induced during yeast-to-hyphal transition. Of these, aconitase and phosphatidylinositol transfer protein were downregulated by HWY-289, suggesting that they mediate the antifungal effects of HWY-289. Finally, RT-PCR analysis revealed that HWY-289 induced expression of three RAS-related genes (CcCST20, CaHST7, and CaCPH1) in yeast cells, but suppressed their expression in hyphae. Thus, the antifungal action of HWY-289 may be attributable to its ability to disrupt prohyphal RAS signaling.
Optimized H.264/AVC-Based Bit Stream Switching for Mobile Video Streaming (2006)

We show the suitability of H.264/MPEG-4 AVC extended profile for wireless video streaming applications. In particular, we exploit the advanced bit stream switching capabilities using SP/SI pictures defined in the H.264/MPEG-4 AVC standard. For both types of switching pictures, optimized encoders are developed. We introduce a framework for dynamic switching and frame scheduling. For this purpose we define an appropriate abstract representation for media encoded for video streaming, as well as for the characteristics of wireless variable bit rate channels. The achievable performance gains over H.264/MPEG-4 AVC with constant bit rate (CBR) encoding are shown for wireless video streaming over enhanced GPRS (EGPRS).
A Continuous Homologation of Esters: An Efficient Telescoped Reduction–Olefination Sequence (2012)

A continuous protocol for the two-carbon homologation of esters to α,β-unsaturated esters is described. This multireactor homologation telescopes an ester reduction, phosphonate deprotonation, and Horner-Wadsworth-Emmons olefination, thus converting a three-operation procedure into a single, uninterrupted system that eliminates the need for isolation or purification of the aldehyde intermediates. The homologated products are obtained in high yield and selectivity.
Covert flow trees: a visual approach to analyzing covert storage channels (1991)

The authors introduce a technique for detecting covert storage channels using a tree structure called a covert flow tree (CFT). CFTs are used to perform systematic searches for operation sequences that allow information to be relayed through attributes and eventually detected by a listening process. When traversed, the paths of a CFT yield a comprehensive list of operation sequences which support communication via a particular resource attribute. These operation sequences are then analyzed and either discharged as benign or determined to be covert communication channels. Algorithms for automating the construction of CFTs and potential covert channel operation sequences are presented. To illustrate this technique, two example systems are analyzed and their results compared to two currently accepted analysis techniques performed on identical systems. This comparison shows that the CFT approach not only identified all covert storage channels found by the other analysis techniques, but discovered a channel not detected by the other techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electronics Work Bench ® And Pspice ® Computer Aided Design Systems As Educational Tools For Second And Fourth Year University Courses In Electronics (2024)

The progress in development of comprehensive computer-aided design (CAD) tools for electronic systems is related to the efficiency of teaching both introductory and advanced courses in electronics at university level. Rapid development of graphical user interface (GUI) created opportunity to convert a personal computer into a virtual electronic development site and thus significantly simplify the applicability of these CAD systems in academic environment. The aim of this study was to compare both qualitatively and quantitatively the student utilization of two of the most popular CAD systems available on today's market, Electronics WorkBench and PSPICE. Twenty-nine second-year students and thirty four fourth-year students taking introductory and advanced courses in Electronics (Department of Electrical and Computer Engineering at the University of Calgary) volunteered to participate in the study, which examined the efficiency of their usage of the two systems in various assignments. The majority of junior students favored exposure to both systems, while the majority of senior students preferred Electronics WorkBench because of its quick learning curve and well-developed GUI environment. We conclude that visual CAD systems for electronic design are very well accepted by students.
Tumor Necrosis Factor Alpha and Pulmonary Function in Saskatchewan Grain Handlers (2006)

These results indicate the complexity of determining which workers will develop acute and chronic adverse pulmonary conditions in response to exposure to grain dust and the toxins in cigarette smoke interacting with their genotype.
Current Trends In A-0 Device Technology For Solid State Picosecond Laser Systems (1987)

The utilization of acousto-optic devices for producing stable picosecond pulses is dis-cussed. Incorporating a highly resonant modelocker in a CW YAG laser, pulse-widths of less than 40 ps were generated at ten watts of average power. In addition a very stable pulse compressor system is described which uses a travelling wave loss modulator to provide 3 ps pulses of 532 nm light at 750 milliwatts of average power and less than 5% peak to peak noise.