gebhart/patrepeval huggingface dataset:
Defect-Aware Synthesis of Droplet-Based Microfluidic Biochips (2007)

Recent advances in microfluidics technology have led to the emergence of miniaturized biochip devices for biochemical analysis. A promising category of microfluidic biochips relies on the principle of electrowetting-on-dielectric, whereby discrete droplets ofnanoliter volumes can be manipulated using an array of electrodes. As chemists adapt more bioassays for concurrent execution on such "digital" droplet-based microfluidic platforms, system integration, design complexity, and the need for defect tolerance are expected to increase rapidly. Automated design tools for defect-tolerant and multifunctional biochips are important for the emerging marketplace, especially for low-cost, portable, and disposable devices for clinical diagnostics. We propose a unified synthesis method that combines defect-tolerant architectural synthesis with defect-aware physical design. The proposed approach allows architectural-level design choices and defect- tolerant physical design decisions to be made simultaneously. We use a large-scale protein assay and the polymerase chain reaction procedure as case studies to evaluate the proposed synthesis method. We also carry out simulations based on defect injection to evaluate the robustness of the synthesized biochip design.
Transcatheter occlusion of the persistently patent ductus arteriosus. Forty-month follow-up and prevalence of residual shunting. (1991)

BACKGROUNDPercutaneous closure of the persistently patent ductus arteriosus with the Rashkind prosthesis is an established effective therapeutic modality, although some patients are left with residual shunting. To evaluate this, a retrospective study of the prevalence of persistent shunting over a 40-month period in the first 190 patients was undertaken.METHODS AND RESULTSAll patients (male 45, female 145; mean age, 3.9 +/- 3.6 years; range, 5 months to 20 years) had serial clinical and color-flow echocardiographic follow-up at 6-12-month intervals (range, 6-40 months). Four patients required surgical removal of an embolized device, leaving a cohort of 186 patients in whom 196 procedures were performed, resulting in successful placement of 195 devices (43 17-mm [22%] and 152 12-mm [78%]). Complications occurred in seven of 195 procedures (3.6%). Nine of 10 attempted reocclusions (all with 12-mm devices) were successful. The prevalence of residual shunting was 38% at 1 year, 18% at 2 years, and 8% at 40 mo...
Structural basis for T cell recognition of altered peptide ligands: a single T cell receptor can productively recognize a large continuum of related ligands. (1996)

T cells recognize short linear peptides bound to major histocompatibility complex (MHC)-encoded molecules. Subtle molecular changes in peptide antigens produce altered peptide ligands (APLs), which induce different T cell responses from those induced by the antigenic ligand. A molecular basis for how these slight molecular variations lead to such different consequences for the T cell has not been described. To address this issue, we have made amino acid substitutions at the primary T cell receptor (TCR) contact residue of the murine hemoglobin determinant, Hb(64-76)/I-Ek and produced 12 peptides that interact with the TCR of the T cell clone 3.L2. The 3.L2 T cell responds to these peptides, which vary 1 million-fold in their activity, and enables them to be ranked according to their relative ability to signal through the 3.L2 TCR. Such a ranking reveals that the ability of the 3.L2 T cell to respond to these peptides depends on how well the structure of the side chain at the primary TCR contact site mimics that of the Asn residue present in the antigenic ligand. The reactivity of the 3.L2 T cell also depends on an MHC contact residue that is next to the primary TCR contact residue, suggesting that conformation of the Asn side chain is also important. By using nonnatural amino acids at a TCR contact residue, we have demonstrated that APLs can be rationally designed based on structure. These data are consistent with a model in which the affinity of a peptide-MHC complex for the TCR determines how the T cell will respond.
Immunoassay Methods -- Assay Guidance Manual (2004)

AimsThis study investigated stress levels and coping strategies among working and nonworking women in the United Arab Emirates.BackgroundStress levels in working and nonworking women have previously been studied, but few studies used cortisol to measure stress or examined how coping strategies affect stress levels.MethodsWe employed a cross-sectional design with a convenience sample of women aged 20–65 years. Information on women’s sociodemographic characteristics, perceived stress (using the Perceived Stress Scale) and coping strategies (using the Brief-COPE) was collected. Participants’ morning (07:00–08:00) and evening (19:00–20:00) cortisol levels were measured using unstimulated saliva samples.ResultsIn total, 417 working and 403 nonworking women participated in this study. More nonworking women reported high stress levels than working women (14.1% vs. 4.1%, p = .001). Working women reported more use of informational support and venting to cope with stress compared with nonworking women (94.0% vs. 88.1%, p = .001). More nonworking women had impaired morning (<0.094 mg/dl) and evening (>0.359 mg/dl) cortisol compared with working women (58.1% vs. 28.5% and 41.7% vs. 18.0%, respectively). Compared with working women, nonworking women had 3.25 (95%CI: 2.38, 4.47) and 3.78 (95%CI: 2.65, 5.43) times the odds of impaired morning and evening cortisol, respectively.ConclusionNonworking women exhibited higher levels of stress than working women. There is an urgent need to support nonworking women to manage stress through appropriate awareness campaigns and public health policies.Implications for ManagementPolicymakers and community leaders should consider the mental health of nonworking women as a priority in planning public health policies and programmes. Nurse managers must have a voice in reforming public health policy to support early assessment and management of stress among nonworking women.
A Chenopod Extensin Lacks Repetitive Tetrahydroxyproline Blocks (1990)

An extensin isolated from sugar beet (Beta vulgaris) cell suspension cultures fulfills all criteria for membership of the extensin family save one, notably, lack of the ;diagnostic' pentamer Ser-Hyp-Hyp-Hyp-Hyp. However, sequence analysis of the major tryptic peptides shows that sugar beet extensin shares a motif in common with tomato extensin P1 but differs by the position of an insertion sequence [X] or [Y] which, in sugar beet, splits the tetrahydroxyproline block: Ser-Hyp-Hyp-[X]-Hyp-Hyp-Thr-Hyp-Val-Tyr-Lys, where [X] is [Val-His-Glu/Lys-Tyr-Pro], while in tomato the insertion sequence [Y] = [Val-Lys-Pro-Tyr-His-Pro] and, when it occurs, immediately follows the tetrahydroxyproline block: Ser-Hyp-Hyp-Hyp-Hyp-[Y]-Thr-Hyp-Val-Tyr-Lys. Based on these data we reinterpret three highly repetitive cDNA sequences, including nodulin N75 from soybean and wound-induced P33 of carrot, as extensins with split tetra(hydroxy)proline blocks.
A distributed certificate management system (DCMS) supporting group-based access controls (2003)

Mainly for scalability reasons, many cryptographic security protocols make use of public key cryptography and require the existence of a corresponding public key infrastructure (PKI). A PKI, in turn, consists of one or several certification authorities (CAs) that issue and revoke certificates for users and other CAs. Contrary to its conceptual simplicity, the establishment and operational maintenance of a CA or PKI has aimed our to be difficult in practice. As a viable alternative, this paper proposes an architecture for a distributed certificate management system (DCMS) that can also be used to provide support for group-based access controls. The architecture has been prototyped and is being used by the Swiss Federal Strategy Unit for Information Technology (FSUIT) to protect access to intranet resources.
Programming Irregular Scientific Algorithms with Static Properties on Clusters of SMP Nodes (2005)

We presented PRFX, an API dedicated to the programming of irregular parallel algorithms with static properties and its runtime support for clusters of SMP nodes. The programming model is based on a task paradigm with implicit synchronizations. These tasks operate on data that are dynamically allocated in an isomemory. The synchronization between tasks is statically computed by an inspector. This allows building data dependencies thanks to a partial pre-execution of the code, and produces a task DAG with all necessary information for the static scheduler and the parallel executor. The parallel executor uses POSIX threads with one-sided communications and works on shared and distributed memory machines. Its performances were validated by experimental results for a sparse Cholesky factorization algorithm on an IBM/sup /spl reg// SP cluster with nodes of 32 Power4 processors.
Immunocompetent Infants as a Human Reservoir for Pneumocystis jirovecii: Rapid Screening by Non‐Invasive Sampling and Real‐Time PCR at the Mitochondria1 Large Subunit rRNA Gene (2003)

We tested a real-time PCR assay targeting the Pneumocystis jirovecii mitochondrial large subunit rRNA gene on 240 archival nasopharyngeal aspirates from non-immunosuppressed infants. The sensitivity of this assay appeared close to that of a conventional nested-PCR assay targeting the same locus. Because of its one-step procedure, and its sensitivity and rapidity, the real-time PCR assay is particularly suitable for screening individuals parasitized by P. jirovecii within large populations.
Expression of Full-length Polyglutamine-expanded Huntingtin Disrupts Growth Factor Receptor Signaling in Rat Pheochromocytoma (PC12) Cells (2002)

We reported previously that normal Huntingtin is associated with epidermal growth factor receptor (EGF) signaling complex (Liu, Y. F., Deth, C. R., and Devys, D. (1997) J. Biol. Chem. 272, 8121-8124). To investigate the potential role of normal and polyglutamine-expanded Huntingtin in the regulation of growth factor receptor-mediated cellular signaling and biological function, we stably transfected full-length Huntingtin containing 16, 48, or 89 polyglutamine repeats into PC12 cells where cellular signaling mechanisms, mediated by nerve growth factor (NGF) or EGF receptors, are well characterized. Expression of polyglutamine-expanded Huntingtin, but not normal Huntingtin, leads to a dramatic morphological change. In clones carrying the mutated Huntingtin, both NGF and EGF receptor-mediated activation of mitogen-activated protein kinase, c-Jun N-terminal kinase, and Akt are significantly attenuated, and NGF receptor-mediated neurite outgrowth is blocked. Co-immunoprecipitation studies show that the associations of NGF or EGF receptors with growth factor receptor-binding protein 2 (Grb2) and phosphoinositide 3-kinase are significantly inhibited. NGF-induced tyrosine phosphorylation of NGF receptors (TrkA) is also consistently suppressed. Our data demonstrate that polyglutamine-expanded Huntingtin disrupts cellular signaling mediated by both EGF and NGF receptors in PC12 cells. It is known that Huntington's disease patients exhibit an extremely low incidence of a variety of cancers and are deficient in glucose metabolism. Thus, our results may reflect an important molecular mechanism for the pathogenesis of the disease.
Alloy Formation in Nanostructured Silicon (2001)

The first systematic study on alloy formation on well-defined nanostructured materialshas been conducted by these authors. Nanostructured silicon and germanium materials were reacted with lithium metal by solid-state chemistry and electrochemical methods, in which nanocrystalline Si (unlike bulk material) forms Li–Si alloys already at room temperature. The Li–Si(Ge) alloys have interesting electrochemical properties, which make them attractive as anode material in lithium batteries.
Hemorrhagic Colitis Associated with a RareEscherichia coliSerotype (1983)

We investigated two outbreaks of an unusual gastrointestinal illness that affected at least 47 people in Oregon and Michigan in February through March and May through June 1982. The illness was characterized by severe crampy abdominal pain, initially watery diarrhea followed by grossly bloody diarrhea, and little or no fever. It was associated with eating at restaurants belonging to the same fast-food restaurant chain in Oregon (P less than 0.005) and Michigan (P = 0.0005) and with eating any of three sandwiches containing three ingredients in common (beef patty, rehydrated onions, and pickles). Stool cultures did not yield previously recognized pathogens. However, a rare Escherichia coli serotype, O157:H7, that was not invasive or toxigenic by standard tests was isolated from 9 of 12 stools collected within four days of onset of illness in both outbreaks combined, and from a beef patty from a suspected lot of meat in Michigan. The only known previous isolation of this serotype was from a sporadic case of hemorrhagic colitis in 1975. This report describes a clinically distinctive gastrointestinal illness associated with E. coli O157:H7, apparently transmitted by undercooked meat.
Sequences of human immunoglobulin switch regions: implications for recombination and transcription (1990)

We have sequenced the entire human S mu and S gamma 4 immunoglobulin heavy chain class switch regions, and have also completed the sequence of human S epsilon. S mu is composed predominantly of GAGCT and GGGCT pentameric repeats, with these units also being found in S epsilon at a much lower density. S mu-S gamma 4 matches are infrequent, but S gamma 4 contains a cluster of repeated sequences similar to units in mouse gamma switch sites and unrelated to the S mu repeats, suggesting that S mu-S gamma homology is not important in mu-gamma switching. We examined our epsilon and gamma 4 sequences for features that could regulate production of 'sterile' transcripts preceding switch recombination. There is an Evolutionarily Conserved Sequence (ECS) upstream from the human and mouse S epsilon regions that overlaps and extends 5' to the start sites for human and mouse epsilon sterile transcripts. Similarly, an ECS upstream from S gamma 4 is homologous to a mouse sequence that overlaps and extends 5' to the start sites for mouse gamma 2b sterile transcripts. The epsilon and gamma 4 conserved segments contain potential Interferon Stimulable Response Elements (ISRE's) that are identical between human epsilon and gamma 4.
Risk Factors for Acute Graft-Versus-Host Disease After Human Leukocyte Antigen–Identical Sibling Transplants for Adults With Leukemia (2008)

This analysis confirmed several previously reported risk factors for grade 2 to 4 acute GVHD. However, several new factors were identified whereas others are no longer significant. These new data may facilitate individualized risk estimates and raise several interesting biologic questions.
Porous-silicon vapor sensor based on laser interferometry (2000)

Certain porous-silicon (PS) films exhibit well-resolved Fabry–Pérot fringes in their optical reflection spectra due to thin-film interference. The fringes shift to higher wavelengths when the PS is exposed to vapors from organic solvents, as a result of an increase in the average refractive index of the PS layer. If a small diode laser is used as the light source, the shift of the Fabry–Pérot fringes upon analyte adsorption results in a change in the reflected light intensity, which correlates with the concentration of the analyte (ethanol) in an air stream. Based on this principle, a PS vapor sensor has been demonstrated with a detection limit of 500 ppb and a dynamic range of nearly five orders of magnitude.
Up-regulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM5 (2008)

Similar to many genes involved in programmed cell death (PCD), the caspase 2 (casp-2) gene generates both proapoptotic and antiapoptotic isoforms by alternative splicing. Using a yeast RNA-protein interaction assay, we identified RBM5 (also known as LUCA-15) as a protein that binds to casp-2 pre-mRNA. In both transfected cells and in vitro splicing assay, RBM5 enhances the formation of proapoptotic Casp-2L. RBM5 binds to a U/C-rich sequence immediately upstream of the previously identified In100 splicing repressor element. Our mutagenesis experiments demonstrate that RBM5 binding to this intronic sequence regulates the ratio of proapoptotic/antiapoptotic casp-2 splicing isoforms, suggesting that casp-2 splicing regulation by RBM5 may contribute to its tumor suppressor activity. Our work has uncovered a player in casp-2 alternative splicing regulation and revealed a link between the alternative splicing regulator and the candidate tumor suppressor gene. Together with previous studies, our work suggests that splicing control of cell death genes may be an important aspect in tumorigenesis. Enhancing the expression or activities of splicing regulators that promote the production of proapoptotic splicing isoforms might provide a therapeutic approach to cancer.
B7–1 Blockade Does Not Improve Post–Transplant Nephrotic Syndrome Caused by Recurrent FSGS (2015)

FSGS is a common glomerular disorder that has a high propensity for recurrence after kidney transplant. The pathophysiology of FSGS is unknown, but podocytes seem to be the target of one or several circulating factors that lead to cytoskeleton reorganization and proteinuria. Research on podocytes has identified B7–1 as an important factor in podocyte biology and a new therapeutic target in renal disease. Indeed, in four patients with recurrent FSGS after transplant, treatment with the B7–1 blocker abatacept was associated with proteinuria remission. Here, we prospectively treated nine patients with recurrent FSGS after transplant using either abatacept or belatacept, a B7–1 blocker with higher affinity, and did not induce proteinuria remission. Furthermore, we did not detect B7–1 expression by immunofluorescence in podocytes of biopsy specimens from these or other kidney grafts or podocytes of native kidney biopsy specimens. In conclusion, B7–1 blockade did not induce FSGS remission after transplant in our study.
Use of circular permutation to assess six bulges and four loops of DNA-packaging pRNA of bacteriophage phi29. (1997)

A 120-base phage phi29 encoded RNA (pRNA) has a novel role in DNA packaging. This pRNA possesses five single-base bulges, one three-base bulge, one bifurcation bulge, one bulge loop, and two stem loops. Circularly permuted pRNAs (cpRNA) were constructed to examine the function of these bulges and loops as well as their adjacent sequences. Each of the five single-base bulges was nonessential. The bifurcation bulge could be deleted and replaced with a new opening to provide flexibility for maintaining an overall correct folding in three-way junction. All of these nonessential bulges or their adjacent bases could be used as new termini for cpRNAs. The three-base (C18C19A20) bulge was dispensable for procapsid binding, but was indispensable for DNA packaging. The secondary structure around this CCA bulge and the phylogenetically conserved bases within or around it were investigated. Bases A14C15U16 were confirmed, by compensatory modification, to pair with U103G102A101. A99 was needed only to allow the proper folding of CCA bulge in the appropriate sequence order and distance constraints. Beyond these, the seemingly phylogenetic conservation of other bases has little role in pRNA activity. Each of the three stem loops was essential for procapsid binding, DNA packaging, and phage assembly. Disruption of the middle of any one of the loops resulted in dramatic reductions in procapsid binding, subsequent DNA packaging, and phage assembly activities. However, disruption of the loops at sequences that were close to double-stranded regions of the RNA did not interfere with pRNA activity significantly. Our results suggest that double-stranded helical regions near these loops were most likely not involved in interactions with components of the DNA-packaging machinery. Instead, these regions appear to be merely present to serve as a scaffolding to display the single-stranded loops that are important for pRNA tertiary structure or for interaction with the procapsid or other packaging components.
On error management: lessons from aviation (2000)

Pilots and doctors operate in complex environments where teams interact with technology. In both domains, risk varies from low to high with threats coming from a variety of sources in the environment. Safety is paramount for both professions, but cost issues can influence the commitment of resources for safety efforts. Aircraft accidents are infrequent, highly visible, and often involve massive loss of life, resulting in exhaustive investigation into causal factors, public reports, and remedial action. Research by the National Aeronautics and Space Administration into aviation accidents has found that 70% involve human error.1

In contrast, medical adverse events happen to individual patients and seldom receive national publicity. More importantly, there is no standardised method of investigation, documentation, and dissemination. The US Institute of Medicine estimates that each year between 44 000 and 98 000 people die as a result of medical errors. When error is suspected, litigation and new regulations are threats in both medicine and aviation.

#### Summary points

In aviation, accidents are usually highly visible, and as a result aviation has developed standardised methods of investigating, documenting, and disseminating errors and their lessons

Although operating theatres are not cockpits, medicine could learn from aviation

Observation of flights in operation has identified failures of compliance, communication, procedures, proficiency, and decision making in contributing to errors

Surveys in operating theatres have confirmed that pilots and doctors have common interpersonal problem areas and similarities in professional culture

Accepting the inevitability of error and the importance of reliable data on error and its management will allow systematic efforts to reduce the frequency and severity of adverse events

Error results from physiological and psychological limitations of humans.2 Causes of error include fatigue, workload, and fear as well as cognitive overload, poor interpersonal communications, imperfect information processing, and flawed decision making.3 In both aviation …