gebhart/patrepeval huggingface dataset:
GC3: An Optimizing Compiler for GPU Collective Communication (2022)

Machine learning models made up of millions or billions of parameters are trained and served on large multi-GPU systems. As models grow in size and execute on more GPUs, the collective communications used in these applications become a bottleneck. Custom collective algorithms optimized for both particular network topologies and application specific communication patterns can alleviate this bottleneck and help these applications scale. However, correctly and efficiently implementing custom algorithms is challenging. This paper introduces GC3, a system for programmable GPU communication. GC3 provides a domain specific language for writing collective communication algorithms and an optimizing compiler for lowering them to an executable form, which can be executed efficiently and flexibly in an interpreter based runtime. We used GC3 to write novel collective algorithms for AllReduce and AllToAll that are up to $1.9\times$ and $1.3\times$ faster than hand-optimized implementations, respectively.
Design, Execution, and Analysis of Time-Varying Experiments for Model Discrimination and Parameter Estimation in Microreactors (2014)

Time-varying, or dynamic, experiments can produce richer data sets than sequences of steady-state experiments using less material and time. A case study demonstrating this concept for microreactor experiments is presented. Beginning with five kinetic model candidates for the reaction of phenylisocyanate with t-butanol, an initial dynamic experiment showed that two of the five models gave a similar quality of fit to the experimental data, whereas the remaining three gave significantly poorer fits. Next an optimal experiment was designed to discriminate between the remaining two models. This drove the two models to differ significantly in quality, leaving a single model and a set of kinetic parameter values that adequately described the data. This method can be applied to future kinetic studies to reduce material use and experimental time while validating a dynamic model of the physics and chemical kinetics.
Collected World and Single Center Experience With Endovascular Treatment of Ruptured Abdominal Aortic Aneurysms (2009)

These results indicate that EVAR has a lower procedural mortality at 30 days than OR in at least some patients and that EVAR is better than OR for treating RAAA patients provided they have favorable anatomy; adequate skills, facilities, and protocols are available; and optimal strategies, techniques, and adjuncts are employed.
Hybridized resonances to design tunable binary phase metasurface unit cells (2014)

The recent concept of metasurfaces is a powerful tool to shape waves by governing precisely the phase response of each constituting element through its resonance properties. While most efforts are devoted to realize reconfigurable metasurfaces that allow such complete phase control, for many applications a binary one is sufficient. Here, we propose and demonstrate through experiments and simulations a binary state tunable phase reflector based on the concept of hybridized resonators as unit cell for a possible metasurface. The concept presents the great advantages to be very general, scalable to all frequency domains and above all very robust to fluctuations induced by the tunable mechanism, as we prove it at microwave frequencies using electronically tunable patch reflectors.
Impedance Analysis of Electrochemical Systems (2022)

Interpretation of impedance spectroscopy data requires both a description of the chemistry and physics that govern the system and an assessment of the error structure of the measurement. The approach presented here includes use of graphical methods to guide model development, use of a measurement model analysis to assess the presence of stochastic and bias errors, and a systematic development of interpretation models in terms of the proposed reaction mechanism and physical description. Application to corrosion, batteries, and biological systems is discussed, and emerging trends in interpretation and implementation of impedance spectroscopy are presented.
Tumor Associated Antigen with Pulmonary Neoplasms (1972)

*Surgical Resident, Department of Surgery, College of Physicians and Surgeons and the Institute for Cancer Research, New York, N. Y. 10032. ** Acting Chairman, Department of Surgery, College of Physicians and Surgeons and the Surgical Service, Presbyterian Hospital, New York, N. Y. 10032. ***Medical Student, 4th year Columbia College of Physicians and Surgeons, Presbyterian Hospital, New York, N. Y. 10032. †Department of Biochemical Nutrition, Hoffmann-La Roche, Nutley, New Jersey 07110.
Positronium in aSrF2single crystal: Temperature-induced transition from the localized to the delocalized state (2005)

Formation of positronium (Ps) in ${\mathrm{SrF}}_{2}$ single crystal is confirmed. Temperature dependence of the momentum distribution and the lifetime of the Ps have been investigated in the temperature range from 10 to 297 K. Temperature induced transition of the Ps from the localized to the delocalized state has been observed. At low temperatures, the Ps is in the localized state. When the temperature is above about 100 K, the Ps in the localized states coexists with that in the delocalized states. The intensity of the delocalized Ps component increases as the temperature rises. The effective mass of the delocalized Ps is found to be $6.3\ifmmode\times\else\texttimes\fi{}2m$, considerably larger than the free Ps mass $(2m)$ in vacuum. The level of the bottom of the delocalized state is 0.012 eV higher than that of the localized state.
An algorithm for planning time-optimal trajectories for given minimum distance paths (2002)

The authors address the problem of determining a time-dependent trajectory when a path planner provides a minimal distance path between two points. In contrast with most of the known methods that work in the velocity-time (v-t) space, theirs works directly in the velocity-arc length (v-s) space, which is the data provided by geometrical path planners. In a first instance, the method assumes a linear path to obtain a nonconstrained trajectory in the v-s plane. The dynamical constraints are then projected into this space to limit the original solution. As the algorithm uses discretized data, the authors provide its cost on space and time and the exact evaluation for the approximation error which depends on the desired accuracy.
Tables S1-S4 from The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations—The Lung Cancer Mutation Consortium (LCMC2) (2023)

&lt;p&gt;Supplemental Table 1. Institutions and PIs participating in LCMC II; Supplemental Table 2. Overview of mutational profiling platforms employed across 16 LCMC2 testing sites; Supplemental Table 3. Mutations in the core genes assayed in LCMC II; Supplemental Table 4. Massively parallel sequencing (MPS) assays employed by LCMCII institutions.&lt;/p&gt;
Illumination of growth, division and secretion by metabolic labeling of the bacterial cell surface (2015)

The cell surface is the essential interface between a bacterium and its surroundings. Composed primarily of molecules that are not directly genetically encoded, this highly dynamic structure accommodates the basic cellular processes of growth and division as well as the transport of molecules between the cytoplasm and the extracellular milieu. In this review, we describe aspects of bacterial growth, division and secretion that have recently been uncovered by metabolic labeling of the cell envelope. Metabolite derivatives can be used to label a variety of macromolecules, from proteins to non-genetically-encoded glycans and lipids. The embedded metabolite enables precise tracking in time and space, and the versatility of newer chemoselective detection methods offers the ability to execute multiple experiments concurrently. In addition to reviewing the discoveries enabled by metabolic labeling of the bacterial cell envelope, we also discuss the potential of these techniques for translational applications. Finally, we offer some guidelines for implementing this emerging technology.
The Utility of Gingival Crevicular Fluid Matrix Metalloproteinase‐8 Response Patterns in Prediction of Site‐Level Clinical Treatment Outcome (2015)

GCF MMP-8 analysis with defined cutoff levels could be used to predict the site-level treatment outcome and for longitudinal monitoring of the disease status during the maintenance period.
Serrated neoplasia in the colorectum: gut microbiota and molecular pathways (2020)

Colorectal cancer (CRC) is a heterogeneous disease with different gene expression patterns. There are two major colorectal carcinogenesis pathways: conventional adenoma-carcinoma pathway and alternative serrated neoplasia pathway. Apart from the conventional pathway that is typically initiated by characteristic <i>APC</i> mutation and chromosomal instability, the serrated neoplasia pathway is mainly characterized by mutations of <i>BRAF</i> or <i>KRAS</i>, microsatellite instability (MSI), and CpG island methylator phenotype (CIMP). Despite the malignant potential of serrated lesions, they can be easily overlooked during endoscopy screening and even in pathological assessment due to its anatomical location, morphology, and histological features. It has been shown that environmental factors especially the gut microbial composition play a key role in CRC pathogenesis. Thus, the preferential localization of serrated lesions in specific intestine areas suggest that niche-specific microbiota composition might intertwined with host genetic perturbations during the development of serrated lesions. Although serrated lesions and conventional adenomas are biologically different, most studies have focused on conventional adenomas, while the pathophysiology and role of microorganisms in the development of serrated lesions remain elusive. In this review, we discuss on the role of gut microbiota in the serrated neoplasia pathway of colorectal carcinogenesis and its specific clinical and molecular features, and summarize the potential mechanisms involved.
Protein secretion in Lactococcus lactis: an efficient way to increase the overall heterologous protein production (2005)

Lactococcus lactis, the model lactic acid bacterium (LAB), is a food grade and well-characterized Gram positive bacterium. It is a good candidate for heterologous protein delivery in foodstuff or in the digestive tract. L. lactis can also be used as a protein producer in fermentor. Many heterologous proteins have already been produced in L. lactis but only few reports allow comparing production yields for a given protein either produced intracellularly or secreted in the medium. Here, we review several works evaluating the influence of the localization on the production yields of several heterologous proteins produced in L. lactis. The questions of size limits, conformation, and proteolysis are addressed and discussed with regard to protein yields. These data show that i) secretion is preferable to cytoplasmic production; ii) secretion enhancement (by signal peptide and propeptide optimization) results in increased production yield; iii) protein conformation rather than protein size can impair secretion and thus alter production yields; and iv) fusion of a stable protein can stabilize labile proteins. The role of intracellular proteolysis on heterologous cytoplasmic proteins and precursors is discussed. The new challenges now are the development of food grade systems and the identification and optimization of host factors affecting heterologous protein production not only in L. lactis, but also in other LAB species.
Parametric Study of Blade Tip Clearance, Flow Rate, and Impeller Speed on Blood Damage in Rotary Blood Pump (2009)

Phenomenological studies on mechanical hemolysis in rotary blood pumps have provided empirical relationships that predict hemoglobin release as an exponential function of shear rate and time. However, these relations are not universally valid in all flow circumstances, particularly in small gap clearances. The experiments in this study were conducted at multiple operating points based on flow rate, impeller speed, and tip gap clearance. Fresh bovine red blood cells were resuspended in phosphate-buffered saline at about 30% hematocrit, and circulated for 30 min in a centrifugal blood pump with a variable tip gap, designed specifically for these studies. Blood damage indices were found to increase with increased impeller speed or decreased flow rate. The hemolysis index for 50-microm tip gap was found to be less than 200-microm gap, despite increased shear rate. This is explained by a cell screening effect that prevents cells from entering the smaller gap. It is suggested that these parameters should be reflected in the hemolysis model not only for the design, but for the practical use of rotary blood pumps, and that further investigation is needed to explore other possible factors contributing to hemolysis.
Learning from the Arabidopsis Experience. The Next Gene Search Paradigm (2001)

Many species have become conscripted for studies in plant biology, with the choices usually driven by considerations such as genetic potential, developmental complexity, or biochemical exclusivity or by a combination of these features. Also, species have been chosen for possessing characteristics of
Infrastructure for Research towards Ubiquitous Information Systems (1994)

The availability of fast, inexpensive computers and the growth of network technology have resulted in the proliferation of computing power and an enormous increase in information available in electronic form. However, most of the information stored on computers is extremely difficult for the common person to obtain. Thus, a central challenge for computer science and engineering in the next decade is to create the scientific and technological base for large-scale and easy-to-use information systems. These systems must work together in a coherent and cohesive manner, providing shared information easily for the general user. We refer to these systems as systems for ubiquitous information. The development of the National Information Infrastructure (NII) amplifies the urgent needs for research in this area. We propose to develop a new generation computing facility to support experimental research in ubiquitous information systems. The research to be carried out using this facility spans from the development of new technologies that support the rapid transmission of large amounts of data between computer systems to the development of more flexible and adaptable systems for human-computer communication. The proposed infrastructure will include emerging equipment with new capabilities critical to this new research, such as Asynchronous Transfer Mode (ATM) networks capable of guaranteeing performance, file servers capable of handling video, and graphics work-stations with advanced human interface capabilities. This equipment will supplement the basic computing and networking equipment typically found in computer science departments.
[Successful readministration of L-asparaginase after development of severe hypertriglyceridemia in a young adult with T-cell acute lymphoblastic leukemia]. (2019)

A 24-year-old male patient with T-cell acute lymphoblastic leukemia was diagnosed with severe hypertriglyceridemia after the sixth administration of L-asparaginase during remission-induction therapy of the Japan Adult Leukemia Study Group (JALSG) -ALL 202-U protocol. Lipoprotein analysis revealed type IV hyperlipidemia, which is associated with a relatively low risk for pancreatitis. Hypertriglyceridemia immediately resolved after discontinuing L-asparaginase and beginning a lipid-restricted diet. The patient did not develop any severe complications of hypertriglyceridemia (e.g., pancreatitis and thrombosis) ; therefore, L-asparaginase could be readministered according to the treatment protocol. Four adult patients with L-asparaginase-induced severe hypertriglyceridemia have been reported to date; however, none of the reports indicated that L-asparaginase had been readministered. Thus, this is the first report of a patient receiving such readministeration. In order to evaluate the safety of continuing L-asparaginase, it is considered necessary to accumulate similar readministration cases.
Combined ac and dc electro-optic response of an azo-dye containing viscoelastic polymer matrix (2003)

We present the combined ac and dc electro-optic response of a model host-guest polymer system. The electro-optic response is found to agree qualitatively with a molecular electric field theory that takes into account the viscoelastic properties of the polymer matrix. Thus, the interaction between the chromophore and the polymer matrix is included into the model for reorientation dynamics. We observe a blue shift in the characteristic electro-optic response as the molecular field is lowered and the chromophore rotates freely. The polymer used for the experiments is Disperse Red 1 containing poly-(methyl methacrylate) (PMMA), and the electro-optic response is measured by means of frequency resolved ellipsometry.
Identification of a Mutation in the Bacillus subtilis S -Adenosylmethionine Synthetase Gene That Results in Derepression of S-Box Gene Expression (2006)

Genes in the S-box family are regulated by binding of S-adenosylmethionine (SAM) to the 5' region of the mRNA of the regulated gene. SAM binding was previously shown to promote a rearrangement of the RNA structure that results in premature termination of transcription in vitro and repression of expression of the downstream coding sequence. The S-box RNA element therefore acts as a SAM-binding riboswitch in vitro. In an effort to identify factors other than SAM that could be involved in the S-box regulatory mechanism in vivo, we searched for trans-acting mutations in Bacillus subtilis that act to disrupt repression of S-box gene expression during growth under conditions where SAM pools are elevated. We identified a single mutant that proved to have one nucleotide substitution in the metK gene, encoding SAM synthetase. This mutation, designated metK10, resulted in a 15-fold decrease in SAM synthetase activity and a 4-fold decrease in SAM concentration in vivo. The metK10 mutation specifically affected S-box gene expression, and the increase in expression under repressing conditions was dependent on the presence of a functional transcriptional antiterminator element. The observation that the mutation identified in this search affects SAM production supports the model that the S-box RNAs directly monitor SAM in vivo, without a requirement for additional factors.
Quasi-zero lattice mismatch and band alignment of BaTiO3 on epitaxial (110)Ge (2013)

Growth, structural, and band alignment properties of pulsed laser deposited amorphous BaTiO3 on epitaxial molecular beam epitaxy grown (110)Ge layer, as well as their utilization in low power transistor are reported. High-resolution x-ray diffraction demonstrated quasi-zero lattice mismatch of BaTiO3 on (110)Ge. Cross-sectional transmission electron microscopy micrograph confirms the amorphous nature of BaTiO3 layer as well as shows a sharp heterointerface between BaTiO3 and Ge with no traceable interfacial layer. The valence band offset, ΔEv, of 1.99 ± 0.05 eV at the BaTiO3/(110)Ge heterointerface is measured using x-ray photoelectron spectroscopy. The conduction band offset, ΔEc, of 1.14 ± 0.1 eV is calculated using the bandgap energies of BaTiO3 of 3.8 eV and Ge of 0.67 eV. These band offset parameters for carrier confinement and the interface chemical properties of the BaTiO3/(110)Ge system are significant advancement towards designing Ge-based p-and n-channel metal-oxide semiconductor field-effect transistors for low-power application.
COVID-19, Diabetes, and Associated Health Outcomes in China: Results from a Nationwide Survey of 10 545 Adults (2021)

This study examined the associations between diabetes and self-reported/familial COVID-19 infection and investigated health-related outcomes among those with diabetes during China's nationwide quarantine. The 2020 China COVID-19 Survey was administered anonymously via social media (WeChat). It was completed by 10 545 adults in all of mainland China's 31 provinces. The survey consisted of 74 items covering sociodemographic characteristics, preventive measures for COVID-19, lifestyle behaviors, and health-related outcomes during the period of quarantine. Regression models examined associations among study variables. Diabetes was associated with a six-fold increased risk of reporting COVID-19 infection among respondents or their family members. Among people with diabetes, individuals who rarely wore masks had double the risk of suspected COVID-19 infection compared with those who always wore masks, with an inverse J-shaped relationship between face mask wearing and suspected COVID-19 infection. People with diabetes tended to have both poor knowledge of COVID-19 and poor compliance with preventive measures, despite perceiving a high risk of personal infection (40.0% among respondents reporting diabetes and 8.0% without diabetes). Only 54-55% of these respondents claimed to consistently practice preventive measures, including wearing face masks. Almost 60% of those with diabetes experienced food or medication shortages during the quarantine period, which was much higher than those without diabetes. Importantly, respondents who experienced medication shortages reported a 63% higher COVID-19 infection rate. Diabetes was associated with an increased risk of self-reported personal and family member COVID-19 infection, which is mitigated by consistent use of face masks.
Complex chemistry of reactive organic compounds. 36. New bridging mode for organodiazo ligands. Molecular structure of (.eta.5-C5H5)(CO)2W(NNMe)Cr(CO)5 (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComplex chemistry of reactive organic compounds. 36. New bridging mode for organodiazo ligands. Molecular structure of (.eta.5-C5H5)(CO)2W(NNMe)Cr(CO)5Gregory L. Hillhouse, Barry L. Haymore, Sabine A. Bistram, and Wolfgang A. HerrmannCite this: Inorg. Chem. 1983, 22, 2, 314–318Publication Date (Print):January 1, 1983Publication History Published online1 May 2002Published inissue 1 January 1983https://doi.org/10.1021/ic00144a022RIGHTS & PERMISSIONSArticle Views56Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (624 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Using Self-Assembled Monolayers to Understand the Interactions of Man-Made Surfaces With Proteins and Cells (1996)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More