gebhart/patrepeval huggingface dataset:
An Insight into the Radical Thiol/Yne Coupling: The Emergence of Arylalkyne-Tagged Sugars for the Direct Photoinduced Glycosylation of Cysteine-Containing Peptides (2010)

An explorative study of the Thiol-Yne Coupling (TYC) reaction has been carried out using an aliphatic (1-octyne) and an aromatic alkyne (phenylacetylene) and two alkanethiols (methyl thioglycolate and N-acetyl-L-cysteine methyl ester). The outcomes of the TYC reactions strongly depend on the experimental conditions (e.g., temperature, solvent, and alkyne/thiol ratio), but these can be properly adjusted to achieve selective production of either mono- or bis-coupling products. With respect to 1-octyne, phenylacetylene undergoes notably easier radical hydrothiolation, further showing a notably higher aptitude for monohydrothiolation exclusive of bis-hydrothiolation. The overall findings were exploited in glycosylation of cysteine derivatives as well as of cysteine-containing peptides. A sugar featuring an arylacetylene moiety gave rise to a true click-reaction, that is, glycosylation of the tripeptide glutathione in its native form, by means of virtually equimolar amounts of reagents. This reaction was successfully applied, under physiological conditions, to a cysteine-containing nonapeptide with marked advantages over the analogous Thiol-Ene Coupling (TEC) derivatization. A TYC/TEC sequence affording bis-armed cysteine derivatives through dual functionalization of an alkynyl sugar was additionally devised.
The Sandiford 2.1-m Cassegrain echelle spectrograph for McDonald Observatory - Optical and mechanical design and performance (1993)

We describe the design, construction, and performance of an efficient new flexure-compensated Cassegrain echelle spectrograph for the 2.1 m (82-inch) Struve reflector at McDonald Observatory. The instrument has a resolving power R = lambda/Delta-lambda of 60,000 for two CCD pixels (for a reciprocal velocity dispersion of 2.5 km s-1 per pixel) and provides continuous wavelength coverage for lambda < 8000 A using a thinned backside illuminated Reticon 1200 X 400 CCD detector. Total wavelength coverage in a single exposure varies from roughly 500 A at lambda = 4400 A (range 4200 - 4700 A) to 2500 A at lambda = 7500 A (range 6500 - 9000 A), and the total system efficiency at lambda = 6000 A from the top of the atmosphere through the telescope, spectrograph, and CCD detector is 10 percent or more. The mechanical design of the Cassegrain-mounted spectrograph incorporates a unique cantilevered counterweight system designed to drastically reduce the effects of gravitational flexure. In spite of the large physical size of the Cassegrain instrument, worst case flexure shifts over 60-degrees (4 hours) of telescope motion are less than 1/2-pixel and are typically on the order of 0.2 pixels or less from all sources. A subsequent paper will describe the CCD and associated electronics in detail.
Irradiation Planning for Fully-Ceramic Micro-encsapsulated fuel in ATR at LWR-relevant conditions: year-end report on FY-2011 (2011)

This report presents the estimation of required ATR irradiation levels for the DB-FCM fuel design (fueled with Pu and MAs). The fuel and assembly designs are those considered in a companion report [R. S. Sen et al., FCR&D-2011- 00037 or INL/EXT-11-23269]. These results, pertaining to the DB-FCM fuel, are definitive in as much as the design of said fuel is definitive. In addition to the work performed, as required, for DB-FCM fuel, work has started in a preliminary fashion on single-cell UO2 and UN fuels. These latter activities go beyond the original charter of this project and although the corresponding work is incomplete, significant progress has been achieved. However, in this context, all that has been achieved is only preliminary because the corresponding fuel designs are neither finalized nor optimized. In particular, the UO2 case is unlikely to result in a viable fuel design if limited to enrichment at or under 20 weight % in U-235. The UN fuel allows reasonable length cycles and is likely to make an optimal design possible. Despite being limited to preliminary designs and offering only preliminary conclusions, the irradiation planning tasks for UO2 and UN fuels that are summarized in this report are useful to the overall goal of devising and deploying FCM-LWR fuel since the methods acquired and tested in this project and the overall procedure for planning will be available for planning tests for the finalized fuel design. Indeed, once the fuel design is finalized and the expected burnup level is determined, the methodology that has been assembled will allow the prompt finalization of the neutronic planning of the irradiation experiment and would provide guidance on the expected experimental performance of the fuel. Deviations from the expected behavior will then have to be analyzed and the outcome of the analysis may be corrections or modifications for the assessment models as well as, possibly, fuel design modifications, and perhaps even variation of experimental control for future experimental phases. Besides the prediction of irradiation times, preliminary work was carried out on other aspects of irradiation planning. In particular, a method for evaluating the interplay of depletion, material performance modeling and irradiation is identified by reference to a companion report. Another area that was addressed in a preliminary fashion is the identification and selection of a strategy for the physical and mechanical design of the irradiation experiments. The principal conclusion is that the similarity between the FCM fuel and the fuel compacts of the Next Generation Nuclear Plant prismatic design are strong enough to warrant using irradiation hardware designs and instrumentation adapted from the AGR irradiation tests. Modifications, if found necessary, will probably be few and small, except as pertains to the water environment and its implications on the use of SiC cladding or SiC matrix with no additional cladding.
Improved Detection of Five Major Gastrointestinal Pathogens by Use of a Molecular Screening Approach (2010)

The detection of bacterial and parasitic gastrointestinal pathogens through culture and microscopy is laborious and time-consuming. We evaluated a molecular screening approach (MSA) for the detection of five major enteric pathogens: Salmonella enterica, Campylobacter jejuni, Giardia lamblia, Shiga toxin-producing Escherichia coli (STEC), and Shigella spp./enteroinvasive E. coli (EIEC), for use in the daily practice of a clinical microbiology laboratory. The MSA consists of prescreening of stool specimens with two real-time multiplex PCR (mPCR) assays, which give results within a single working day, followed by guided culture/microscopy of the positive or mPCR-inhibited samples. In the present 2-year overview, 28,185 stool specimens were included. The MSA was applied to 13,974 stool samples (49.6%), whereas 14,211 samples were tested by conventional methods only (50.4%). The MSA significantly increased the total detection rate compared to that of conventional methods (19.2% versus 6.4%). The detection of all included pathogens, with the exception of S. enterica, significantly improved. MSA detection frequencies were as follows: C. jejuni, 8.1%; G. lamblia, 4.7%; S. enterica, 3.0%; STEC, 1.9%; and Shigella spp./EIEC, 1.4%. The guided culture/microscopy was positive in 76.8%, 58.1%, 88.9%, 16.8%, and 18.1% of mPCR-positive specimens, respectively. Of all mPCRs, only 1.8% was inhibited. Other findings were that detection of mixed infections was increased (0.9% versus 0.02%) and threshold cycle (C(T)) values for MSA guided culture/microscopy-positive samples were significantly lower than those for guided culture/microscopy-negative samples. In conclusion, an MSA for detection of gastrointestinal pathogens resulted in markedly improved detection rates and a substantial decrease in time to reporting of (preliminary) results.
Protein kinase CK2 and its role in cellular proliferation, development and pathology (1999)

Protein kinase CK2 is a pleiotropic, ubiquitous and constitutively active protein kinase that can use both ATP and GTP as phosphoryl donors with specificity for serine/threonine residues in the vicinity of acidic amino acids. Recent results show that the enzyme is involved in transcription, signaling, proliferation and in various steps of development. The tetrameric holoenzyme (alpha2beta2) consists of two catalytic alpha-subunits and two regulatory beta-subunits. The structure of the catalytic subunit with the fixed positioning of the activation segment in the active conformation through its own aminoterminal region suggests a regulation at the transcriptional level making a regulation by second messengers unlikely. The high conservation of the catalytic subunit from yeast to man and its role in the tetrameric complex supports this notion. The regulatory beta-subunit has been far less conserved throughout evolution. Furthermore the existence of different CK2beta-related proteins together with the observation of deregulated CK2beta levels in tumor cells and the reported association of CK2beta protein with key proteins in signal transduction, e.g. A-Raf, Mos, pg90rsk etc. are suggestive for an additional physiological role of CK2beta protein beside being the regulatory compound in the tetrameric holoenzyme.
A Novel Three-Component Reaction of Allenoates, Isocyanides, and Carboxylic Acids:  Facile Synthesis of Highly Substituted Acryl Imide Derivatives (2008)

A novel synthesis of highly substituted acryl imide derivatives by the three-component reaction of allenoates, isocyanides, and carboxylic acids was reported, and the intramolecular cyclization reaction of allenoic acids with isocyanides was also described.
How to perform subsequent or ‘double’ immunostaining of two different antigens on a single nitrocellulose blot within one day with and immunoperoxidase technique (1984)

Abstract Defining the properties of antibody preparations has been facilitated by immunoblotting techniques: by ‘double’ immunostaining of blots, however, one can clearly visualize the properties of two (or even more) antibodies on a single blot. We describe a one‐day procedure in which two different antisera, both raised in rabbits, can subsequently be applied to a single nitrocellulose blot of protein samples separated by either native or sodium dodecyl sulfate‐polyacrylamide gradient gel electrophoresis. In order to visualize antibody activity, a three‐step unlabeled immunoezyme method ‐ the peroxidase anti‐peroxidase technique ‐ has been used for both first and second immunostaining. Discrimination between the results of each of the immunostainings has been achieved by using 3,3′ ‐diaminobenzidine and 4‐chloronaphtol as different peroxidase substrates which yield differently colored precipitates. The problem of method overlapping has been overcome by developing a short but efficient elution procedure for the elution of antibody bound to the blot during the first immunostaining: going from ‘mild’ conditions (suited for incubations with sera) to ‘denaturing’ conditions (low pH, low ionic strength, 20 % dimethylformamide) and vice versa repeatedly does not affect antigens but elutes antibodies completely.
A N-best sentence hypotheses enumeration algorithm with duration constraints based on the two level algorithm (2003)

A new N-best sentence hypotheses enumeration algorithm for continuous speech recognition that correctly incorporates duration constraints and which is very efficient in practice is presented. Based on the most general two-level procedure, this algorithm provides greater flexibility in acoustic modeling than previous approaches and is very well suited for large vocabulary applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Wideband efficiency improvement of fiber optic systems by carrier subtraction (1995)

Carrier subtraction from a weakly modulated optical signal is proposed, analyzed, and demonstrated to improve fiber-optic system efficiency. For constant photodetector current, an amount of carrier suppression results in an equal amount of RF gain. Improvement of 9-13 dB in link loss from 1 to 25 GHz is measured using a Fabry-Perot filter operating in the reflection mode. Measured induced harmonic distortion agrees with predicted values.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
4-Hydroperoxycyclophosphamide purged autologous bone marrow transplantation in non-Hodgkin's lymphoma patients at high risk of bone marrow involvement. (1996)

Between June 1990 and January 1994, 19 patients with non-Hodgkin's lymphoma (NHL) at high risk for bone marrow involvement underwent 4-hydroperoxycyclophosphamide (4-HC) purged bone marrow transplantation. Eleven patients had low grade, seven intermediate grade and one high grade NHL and 7/19 patients had received three or more previous chemotherapeutic regimens. Four patients were transplanted in first partial remission (PR) and the remainder in responsive relapse. Fourteen patients had bone marrow (BM) involvement at diagnosis and/or at relapse. The median times to granulocyte and platelet recovery were 26 and 29 days, respectively. There were two toxic deaths and one complete responder developed secondary AML at 31 months post-BMT. Seventeen of 18 evaluable patients achieved a complete remission (CR) and one patient a PR. Fourteen patients (74%) are progression-free at a median follow-up of survivors of 34 months (range 29-55). The 3 year event-free (EFS) and overall survival (OS) probabilities are both 67%. No statistically significant difference was seen between EFS or OS and BM involvement or histologic grade at diagnosis. At 29 months, 4/7 patients with a morphologically involved BM harvest had relapsed or died compared to 1/12 patients with negative BM (P = 0.03). These results are encouraging and warrant further investigation of 4-HC purging in NHL.
Applications of the maximum entropy method to powder diffraction and electron crystallography (1993)

Abstract A new multisolution phasing method based on entropy maximization and likelihood ranking, proposed for the specific purpose of increasing the accuracy and sensitivity of probabilistic phase indications compared with conventional direct methods, has been implemented and applied to a wide variety of problems. The latter comprise the determination of small crystal structures from X-ray diffraction data obtained from single crystals or from powders, and from electron diffraction data, both with and without partial phase information obtained by image processing of electron micrographs; the ranking of phase sets for a small protein; and the improvement of poor quality phases for a larger protein at medium resolution under constraint of solvent flatness. The main components of the method are (1) a tree-directed search through a space of trial phase sets; (2) the saddlepoint method for calculating joint probabilities of structure factors, using entropy maximization; (3) likelihood-based scores to rank trial phase sets and prune the search tree; (4) a statistical analysis of the scores for automatically selecting reliable phase indications. Their use is illustrated here on structure determinations from powder X-ray diffraction data and from electron diffraction data.
Construction of an Escherichia coli-Clostridium perfringens shuttle vector and plasmid transformation of Clostridium perfringens (1989)

A stable shuttle vector which replicates in Escherichia coli and Clostridium perfringens was constructed by ligating a 3.6-kilobase (kb) fragment of plasmid pBR322 with C. perfringens plasmid pHB101 (3.1 kb). The marker for this shuttle plasmid originated from the 1.3-kb chloramphenicol resistance gene of plasmid pHR106. The resulting shuttle vector, designated pAK201, is 8 kb in size and codes for resistance to 20 micrograms of chloramphenicol per ml in both E. coli and C. perfringens. Following shuttle vector construction in E. coli, plasmid pAK201 was transformed into E. coli HB101 and C. perfringens ATCC 3624A, using intact cell electroporation. The transformation frequencies were 10(6) and 10(4) transformants per microgram of DNA in E. coli and C. perfringens, respectively. Restriction enzyme analysis of the chimera isolated from transformants of both microorganisms suggested that the plasmids were identical. Reciprocal transformation experiments in E. coli and C. perfringens indicated no difference in transformation frequency. Plasmid pAK201 was stable in C. perfringens following repeated transfer in the absence of chloramphenicol pressure. The restriction map of plasmid pAK201 shows six unique cut sites which should be useful for future genetic analysis and C. perfringens gene library construction.
Molecular identification of <i>spadetail:</i> regulation of zebrafish trunk and tail mesoderm formation by T-box genes (1998)

Inhibition of fibroblast growth factor (FGF) signaling prevents trunk and tail formation in Xenopus and zebrafish embryos. While the T-box transcription factor Brachyury (called No Tail in zebrafish) is a key mediator of FGF signaling in the notochord and tail, the pathways activated by FGF in non-notochordal trunk mesoderm have been uncertain. Previous studies have shown that the spadetail gene is required for non-notochordal trunk mesoderm formation; spadetail mutant embryos have major trunk mesoderm deficiencies, but relatively normal tail and notochord development. We demonstrate here that spadetail encodes a T-box transcription factor with homologues in Xenopus and chick. Spadetail is likely to be a key mediator of FGF signaling in trunk non-notochordal mesoderm, since spadetail expression is regulated by FGF signaling. Trunk and tail development are therefore dependent upon the complementary actions of two T-box genes, spadetail and no tail. We show that the regulatory hierarchy among spadetail, no tail and a third T-box gene, tbx6, are substantially different during trunk and tail mesoderm formation, and propose a genetic model that accounts for the regional phenotypes of spadetail and no tail mutants.
Mutations predisposing to breast cancer in 12 candidate genes in breast cancer patients from Poland (2014)

A number of genes other than BRCA1 and BRCA2 have been associated with breast cancer predisposition, and extended genetic testing panels have been proposed. It is of interest to establish the full spectrum of deleterious mutations in women with familial breast cancer.We performed whole-exome sequencing of 144 women with familial breast cancer and negative for 11 Polish founder mutations in BRCA1, CHEK2 and NBS1, and we evaluated the sequences of 12 known breast cancer susceptibility genes. A truncating mutation in a breast cancer gene was detected in 24 of 144 women (17%) with familial breast cancer. A BRCA2 mutation was detected in 12 cases, a (non-founder) BRCA1 mutation was detected in 5 cases, a PALB2 mutation was detected in 4 cases and an ATM mutation was detected in 2 cases. Polish women with familial breast cancer who are negative for founder mutations in BRCA1, CHEK2 and NBS1 should be fully screened for mutations in BRCA1, BRCA2 and PALB2. The PALB2 founder mutation c.509_519delGA should be included in the panel of Polish founder mutations.
Can Music Make You Sick? Measuring the Price of Musical Ambition (2021)

In recent media texts, the plight of popular musicians and their mental health has been prominent. From Jesy Nelson leaving the British girl group Little Mix to focus on her mental health, to dance...
RIDE-QUALITY MODELS FOR DIVERSE TRANSPORTATION SYSTEMS (1980)

This research was undertaken to develop comfort (ride-quality) models for six specific vehicles and to refine an existing composite ride-quality model. The vehicles were an automated guideway transit vehicle, a short-haul intercity rail vehicle, an urban rapid rail vehicle, a luxury-type charter bus, a compact car, and a subcompact automobile. Experiments on most vehicles were conducted in two phases: model development and model validation. In both phases, physical variables were measured for a series of ride segments, and each segment was rated for comfort level by a group of paid subjects. The important determinants of comfort for most vehicles were roll, pitch, and vertical acceleration. These variables are highly intercorrelated; all load on the same principal component of the motion-correlation matrix. Two composite ride-quality models are presented; one has four variables (roll, pitch, and vertical and longitudinal acceleration) and one has two variables (vertical acceleration and roll). The two-variable comfort model is sufficient for most uses. (Author)
TCP/IP traffic dynamics and network performance (2001)

The main objective of this paper is to demonstrate in the context of a simple TCP/IP-based network that depending on the underlying assumptions about the inherent nature of the dynamics of network traffic, very different conclusions can be derived for a number of well-studied and apparently well-understood problems in the area of performance evaluation. For example, a traffic workload model can either completely ignore the empirically observed high variability at the TCP connection level (i.e., assume "infinite sources") or explicitly account for it with the help of heavy-tailed distributions for TCP connection sizes or durations. Based on detailed ns-2 simulation results, we illustrate that these two commonly-used traffic workload scenarios can give rise to fundamentally different buffer dynamics in IP routers. Using a second set of ns-2 simulation experiments, we also illustrate a qualitatively very different queueing behavior within IP routers depending on whether the traffic arriving at the router is assumed to be endogenous in nature (i.e., a result of the "closed loop" nature of the feedback-based congestion control algorithm of TCP) or exogenously determined (i.e., given by some conventional traffic model --- a fixed "open loop" description of the traffic as seen by the router).
Allocating time and resources in project management under uncertainty (2003)

We define and develop a solution approach for planning, scheduling and managing project efforts where there is significant uncertainty in the duration, resource requirements and outcomes of individual tasks. Our approach yields a nonlinear optimization model for allocation of resources and available time to tasks. This formulation represents a significantly different view of project planning from the one implied by traditional project scheduling, and focuses attention on important resource allocation decisions faced by project managers. The model can be used to maximize any of several possible performance measures for the project as a whole. We include a small computational example that focuses on maximizing the probability of successful completion of a project whose tasks have uncertain outcomes. The resource allocation problem formulated here has importance and direct application to the management of a wide variety of project-structured efforts where there is significant uncertainty.
Engineered Microvessels for the Study of Human Disease (2016)

The microvasculature is an extensive, heterogeneous, and complex system that plays a critical role in human physiology and disease. It nourishes almost all living human cells and maintains a local microenvironment that is vital for tissue and organ function. Operating under a state of continuous flow, with an intricate architecture despite its small caliber, and subject to a multitude of biophysical and biochemical stimuli, the microvasculature can be a complex subject to study in the laboratory setting. Engineered microvessels provide an ideal platform that recapitulates essential elements of in vivo physiology and allows study of the microvasculature in a precise and reproducible way. Here, we review relevant structural and functional vascular biology, discuss different methods to engineer microvessels, and explore the applications of this exciting tool for the study of human disease.