gebhart/patrepeval huggingface dataset:
Assembling Large DNA Segments in Yeast (2012)

As described in a different chapter in this volume, the uracil-specific excision reaction (USER) fusion method can be used to assemble multiple small DNA fragments (∼0.75-kb size) into larger 3-kb DNA segments both in vitro and in vivo (in Escherichia coli). However, in order to assemble an entire synthetic yeast genome (Sc2.0 project), we need to be able to assemble these 3-kb pieces into larger DNA segments or chromosome-sized fragments. This assembly into larger DNA segments is carried out in vivo, using homologous recombination in yeast. We have successfully used this approach to assemble a 40-kb chromosome piece in the yeast Saccharomyces cerevisiae. A lithium acetate (LiOAc) protocol using equimolar amount of overlapping smaller fragments was employed to transform yeast. In this chapter, we describe the assembly of 3-kb fragments with an overlap of one building block (∼750 base pairs) into a 40-kb DNA piece.
Ultrasound Doppler Probing of Flows Transverse with Respect to Beam Axis (1987)

It is an accepted fact that transverse Doppler effects of the first order in v/c are nonexistent for all physical wave phenomena, including acoustics, i.e., the Doppler effect is zero for radiation normal to the direction of motion. However, this statement assumes that the incident field is a plane wave, which is not true in general for finite aperture sources. Consequently, the probing of flows transverse to the axis of finite diameter beams, particularly focused beams, is feasible. This geometry will be advantageous in many applications where the classical orientation of the sound beam, oblique to the flow, is not possible. With this motivation in mind, the theory and experimental feasibility of measuring Doppler spectra in transverse geometries is presently investigated.
Structure−Activity Relationship Analysis of the Selective Inhibition of Transglutaminase 2 by Dihydroisoxazoles (2006)

Human transglutaminase 2 (TG2) is believed to play an important role in the pathogenesis of various human disorders including celiac sprue, certain neurological diseases, and some types of cancer. Selective inhibition of TG2 should therefore enable further investigation of its role in physiology and disease and may lead to effective clinical treatment. Recently we showed that certain 3-halo-4-,5-dihydroisoxazole containing compounds are selective inhibitors of human TG2 with promising pharmacological activities. Here, we present definitive evidence that this class of compounds targets the active site of human TG2. Structure-activity relationship studies have provided insights into the structural prerequisites for selectivity and have led to the discovery of an inhibitor with about 50-fold higher activity than a prototypical dihydroisoxazole inhibitor with good in vivo activity. A method for preparing enantiomerically enriched analogues was also developed. Our studies show that the 5-(S)-dihydroisoxazole is a markedly better inhibitor of human TG2 than its 5-(R) stereoisomer.
TNF- downregulates eNOS expression and mitochondrial biogenesis in fat and muscle of obese rodents (2006)

Obesity is associated with chronic low-grade inflammation. Thus, at metabolically relevant sites, including adipose tissue and muscle, there is abnormal production of proinflammatory cytokines such as TNF-alpha. Here we demonstrate that eNOS expression was reduced, with a concomitant reduction of mitochondrial biogenesis and function, in white and brown adipose tissue and in the soleus muscle of 3 different animal models of obesity. The genetic deletion of TNF receptor 1 in obese mice restored eNOS expression and mitochondrial biogenesis in fat and muscle; this was associated with less body weight gain than in obese wild-type controls. Furthermore, TNF-alpha downregulated eNOS expression and mitochondrial biogenesis in cultured white and brown adipocytes and muscle satellite cells of mice. The NO donors DETA-NO and SNAP prevented the reduction of mitochondrial biogenesis observed with TNF-alpha. Our findings demonstrate that TNF-alpha impairs mitochondrial biogenesis and function in different tissues of obese rodents by downregulating eNOS expression and suggest a novel pathophysiological process that sustains obesity.
Sonic Analysis of the Redlands UFO Tape Recording (2016)

The February 4, 1968 UFO sighting at Redlands, CA was accompanied by an intense, distinctive sound that was recorded as a background sound on a magnetic tape recording being made by Reverend Julian Vigh at the Bethel Christian Church. A rescue Emergency Vehicle (EV), with its siren operating, happened to be deployed in Redlands at the time of the UFO sightings. An informal inquiry by several Redlands University professors attributed the background sound on the Vigh recording to the EV siren. Subsequently, I performed independent comprehensive detailed sonic analyses of the tape background sound and the EV siren, and documented these analyses in a 1969 report intended for inclusion as an independent technical appendix in a book on the Redlands UFO sightings then in preparation by authors David Branch and Robert Klinn. This book was never completed and published. The independent technical appendix is released and published here for the first time. Detailed tape analyses revealed and quantified a number of sonic anomalies. Present day concluding comments are offered that place these anomalies in the context of other investigative reports of the Redlands UFO sightings that appeared in the press subsequent to the writing of the appendix in 1969.
Static versus Expandable Interbody Fusion Devices: A Comparison of 1-Year Clinical and Radiographic Outcomes in Minimally Invasive Transforaminal Lumbar Interbody Fusion (2022)

Expandable devices provide greater improvements in radiographic measurements including anterior disk height, posterior disk height, and segmental lordosis, but this did not lead to significant improvements in PROMs, complication rates, subsidence rates, or subsidence distance.
Long term efficacy of repeat selective laser trabeculoplasty (2014)

Repeat SLT is effective in lowering IOP up to 24 months. Long term IOP control was achieved in 29-39% of eyes following repeat treatment in this cohort of patients.
Effect of pulmonary perfusion on the slopes of single-breath test of CO2 (2005)

The objective of this study was to evaluate the effects of lung perfusion on the slopes of phases II (S(II)) and III (S(III)) of a single-breath test of CO(2) (SBT-CO(2)). Fourteen patients submitted to cardiac surgery were studied during weaning from cardiopulmonary bypass (CPB). Pump flow was decreased in 20% steps, from 100% (total CPB = 2.5 l.min(-1).m(-2)) to 0%. This maneuver resulted in a progressive and opposite increase in pulmonary blood flow (PBF) while maintaining ventilator settings constant. SBT-CO(2), respiratory, and hemodynamic variables remained unchanged before and after CPB, reflecting a constant condition at those stages. S(III) was similar before and after CPB (19.6 +/- 2.8 and 18.7 +/- 2.1 mmHg/l, respectively). S(III) was lowest during 20% PBF (8.6 +/- 1.9 mmHg/l) and increased in proportion to PBF until exit from CPB (15.6 +/- 2.2 mmHg/l; P < 0.05). Similarly, S(II) and the CO(2) area under the curve increased from 163 +/- 41 mmHg/l and 4.7 +/- 0.6 ml, respectively, at 20% PBF to 313 +/- 32 mmHg/l and 7.9 +/- 0.6 ml (P < 0.05) at CPB end. When S(II) and S(III) were normalized by the mean percent expired CO(2), they remained unchanged during the protocol. In summary, the changes in PBF affect the slopes of the SBT-CO(2). Normalizing S(II) and S(III) eliminated the effect of changes in the magnitude of PBF on the shape of the SBT-CO(2) curve.
ChemInform Abstract: PHOTOREDUCTION OF THIOSULFATE IN SEMICONDUCTOR DISPERSIONS (1983)

Abstract Durch Bandlückenanregung von TiOg‐Teilchen erzeugte Leitungsbandelektronen reduzieren S203′ gemäß Reaktion A zu S2′ und S03′.
Effects of Sex and Type of Humor on Humor Appreciation (1981)

Examined humor appreciation of cartoons as a function of sex of subject and type of humor. Four broad types of humor were presented: sexual-exploitative, sexual-nonexploitative, nonsexual-hostile, and nonsexual-nonhostile. Sexual-nonexploitative humor was rated as funnier than the other three types but nonsexual-nonhostile humor was given a more positive overall rating than the other types. Relative to males, females gave greater ratings of hostility to the cartoons and rated them less positively. Correlational analyses further suggested that females were not as affected as males by variations in sexuality, exploitation, and hostility. For males, greater ratings of sexuality were associated with greater funniness ratings while the reverse was true for greater ratings of hostility. Possible interpretations of these data were discussed.
Reliability improvement in multicore architectures through computing in embedded memory (2011)

Nanoscale devices provide the capability of gigascale integration in modern electronic systems. However, such systems suffer from high defect rates and large parametric variations that can adversely affect system reliability. Hardware duplication is an obvious direction but it incurs significant area overhead that is unacceptable in many scenarios. Memory-based computing (MBC) is a promising alternative to improve overall system reliability when few functional units are defective or unreliable under process-induced or thermal variations. Existing works demonstrated the utility of MBC in single-core based designs. In this paper, we explore the effectiveness of MBC in multicore architectures where each core uses a small private cache while a set of cores share a large second-level cache. The private as well as shared caches are used to perform computation on demand using a lookup table. When a functional unit fails, temporarily due to temperature induced variations or permanently, the associated computation is transferred to caches. Experimental results demonstrate that on-demand memory based computing can significantly improve reliability with minor loss in performance.
Biconvex Patellar Components (2021)

Background: The optimal strategy to address osseous deficiencies of the patella during revision total knee arthroplasty (TKA) remains controversial. One possible solution is a cemented biconvex patellar component used such that the non-articular convexity both improves fixation and makes up for bone loss. The aim of this study was to determine the outcomes of the use of biconvex patellar components in a large series of revision TKAs. Methods: From 1996 to 2014, 262 revision TKAs were performed at a single institution using a biconvex patellar component. Implant survivorship, clinical and radiographic results, and complications were assessed. The mean patient age at the TKA revision was 69 years, and 53% of the patients were female. The mean follow-up was 7 years. Results: The 10-year survivorship free of revision of the biconvex patellar component due to aseptic loosening was 96%. The 10-year survivorship free of any revision of the biconvex patellar component was 87%. The 10-year survivorship free of any rerevision and free of any reoperation was 75% and 70%, respectively. The mean Knee Society Score (KSS) improved from 45.4 before the index revision to 67.7 after it. The mean residual composite thickness seen on the most recent radiographs was 18.1 mm. In addition to the complications leading to revision, the most common complications were periprosthetic patellar fracture (6%), of which 3 required revision; superficial wound infection (6%) requiring antibiotic therapy only or irrigation and debridement; and arthrofibrosis (3%). Conclusions: In this cohort of 262 revision TKAs, biconvex patellar components used to treat marked patellar bone loss demonstrated excellent durability with a 10-year survivorship free of patellar rerevision due to aseptic loosening of 96%. The biconvex patellar components were reliable as evidenced by substantial improvements in clinical outcomes scores and a low risk of complications. Level of Evidence: Therapeutic Level IV . See Instructions for Authors for a complete description of levels of evidence.
Critical Reliability Issues for SiC Power MOSFETs Operated at High Temperature (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Recognition of β-Ketoalcohol-derived Haptens by Tailor-made Antibodies (2001)

Antibodies steamed from mice immunized towards three different conjugates do not recognize the b-ketoalcohol for which they have been elaborated. They however recognize the haptens, which bear the side chain linking them to the carrier proteins. We have synthesized and tested for recognition a series of compounds related to those haptens, especially stereoisomers and compounds bearing part of their structures. Results and hypotheses are presented below.
Distribution of killer‐cell immunoglobulin‐like receptor (KIR) in Comoros and Southeast France (2006)

Killer-cell immunoglobulin-like receptors (KIRs) expressed by natural killer cells are cell surface molecules able to recognize groups of HLA class I alleles. The number and distribution of KIR genes vary among individuals and populations. The aim of this study is to analyse the KIR gene content in a Comorian population in order to investigate genetic relationships with other populations and to reconstruct past migration events. The Comorian population consisted of 54 unrelated immigrants living in France and a control population consisted of 38 individuals from Southeast France. We investigated the presence or absence of 15 KIR genes, two pseudogenes expressed and non-expressed forms of KIR2DL5 and the two major subtype full-length and deleted forms of KIR2DS4. All individuals were typed positive for the framework genes, i.e. KIR2DL4, KIR3DL2 and KIR3DL3, and the two pseudogenes KIR3DP1 and KIR2DP1. The frequencies of full-length KIR2DS4 (*00101/00102/002) were lower in the French population (F = 29%) than in the Comorian population (F = 72%) (P(c) < 0.05). No significant differences were found for other KIR genes. A total of 11 genotypes were identified in the Southeast French population and 22 genotypes in the Comorian population. The most common genotype (2DL1, 2DL3, 2DL4, 3DL1, 3DL2, 3DL3 and 2DS4) accounted for 41% in the Comorian population and 34% in the Southeast French population. Principal component analysis using KIR gene data from 20 populations was performed to determine genetic differences and relations between populations. The Comorian population exhibited closest kinship with Africans and Asians. As KIR gene content is heterogeneous among ethnic groups, it can probably be used to assess the genetic relationships among populations from different geographic areas.
Noncanonical role for Ku70/80 in the prevention of allergic airway inflammation via maintenance of airway epithelial cell organelle homeostasis (2020)

Airway epithelial homeostasis is under constant threat due to continuous exposure to the external environment, and abnormally robust sensitivity to external stimuli is critical to the development of airway diseases, including asthma. Ku is a key nonhomologous end-joining DNA repair protein with diverse cellular functions such as VDJ recombination and telomere length maintenance. Here, we show a novel function of Ku in alleviating features of allergic airway inflammation via the regulation of mitochondrial and endoplasmic reticulum (ER) stress. We first determined that airway epithelial cells derived from both asthmatic lungs and murine asthma models demonstrate increased expression of 8-hydroxy-deoxyguanosine (8-OHdG), a marker of oxidative DNA damage. Ku protein expression was dramatically reduced in the bronchial epithelium of patients with asthma as well as in human bronchial epithelial cells exposed to oxidative stress. Knockdown of Ku70 or Ku80 in naïve mice elicited mitochondrial collapse or ER stress, leading to bronchial epithelial cell apoptosis and spontaneous development of asthma-like features, including airway hyperresponsiveness, airway inflammation, and subepithelial fibrosis. These findings demonstrate an essential noncanonical role for Ku proteins in asthma pathogenesis, likely via maintenance of organelle homeostasis. This novel function of Ku proteins may also be important in other disease processes associated with organelle stress.
Teflon Spray Ionization Mass Spectrometry (2020)

Polytetrafluoroethene, commonly known as Teflon, is a plastic famous for its inertness, strength, and nonstick properties, allowing its repeated use in many applications. We report the use of a triangularly cut Teflon substrate to take the place of paper in a form of spray mass spectrometry. A conducting wire (gold) at high potential (positive or negative) makes contact with a drop of the liquid sample at the apex of the triangle, causing a spray of droplets to be directed toward the heated inlet of a mass spectrometer. Saccharides, drugs, illegal additives, peptides, proteins, bilirubin, and vancomycin give mass spectra with high signal-to-noise (S/N) ratios, allowing detection at the nanogram per milliliter (ng/mL) level. Examination of each of these analytes demonstrates that Teflon spray is several orders of magnitude more sensitive than paper spray under the same conditions. Teflon spray ionization mass spectrometry is applied to the metabolomic and lipidomic profiling of biological fluid samples. Detection of polycyclic aromatic hydrocarbons is achieved with Teflon spray at 10 μg/mL concentrations. These experiments show the advantage of using Teflon over a normal paper substrate in detecting many environmentally and biologically relevant systems with high sensitivity and S/N ratio.
Improved Accuracy of Unguided Articulated Robots (2009)

&lt;div class="htmlview paragraph"&gt;The effectiveness of serial link articulated robots in aerospace drilling and fastening is largely limited by positional accuracy. Unguided production robotic systems are practically limited to +/-0.5mm, whereas the majority of aerospace applications call for tolerances in the +/-0.25mm range. The precision with which holes are placed on an aircraft structure is affected by two main criteria; the volumetric accuracy of the positioner, and how the system is affected when an external load is applied. Production use and testing of off-the-shelf robots has highlighted the major contributor to reduced stiffness and accuracy as being error ahead of the joint position feedback such as backlash and belt stretch. These factors affect the omni-directional repeatability, thus limiting accuracy, and also contribute to deflection of the tool point when process forces are applied. Drawing from common axis configuration in machine tool design, an industrial robot integrated with secondary encoders yields tighter control on axis position and increases system rigidity, thus creating a more repeatable system and, in turn, a system than can be compensated to high accuracies.&lt;/div&gt;
Analysis of Explicit vs. Implicit Tasking in OpenMP Using Kripke (2018)

Dynamic task-based parallelism has become a widely-accepted paradigm in the quest for exascale computing. In this work, we deliver a non-trivial demonstration of the advantages of explicit over implicit tasking in OpenMP 4.5 in terms of both expressiveness and performance. We target the Kripke benchmark, a mini-application used to test the performance of discrete particle codes, and find that the dependence structure of the core “sweep” kernel is well-suited for dynamic task-based systems. Our results show that explicit tasking delivers a 31.7% and 8.1% speedup over a pure implicit implementation for a small and large problem, respectively, while a hybrid variant also underperforms the explicit variant by 13.1% and 5.8%, respectively.
Multitarget stool DNA test: clinical performance and impact on yield and quality of colonoscopy for colorectal cancer screening (2016)

Knowledge of a positive MT-sDNA result appears to have a beneficial impact on the diagnostic yield and quality of subsequent colonoscopy.
A DECT testbed for applications and services studies (1991)

A testbed of for the DECT system has been constructed and the basic concepts of the DECT radio specification have been validated. The testbed is proving to be a flexible and valuable tool for developing applications and services. >
CHRIST IS RISEN! INDEED HE IS RISEN! (2015)

ON THE MEND: Please keep the following parishioners and others in your prayers for recovery from their illnesses and injuries: Metropolitan Constantine, Patriarch Pavle, Metropolitan Theodosius, Bishop Robert, Father Peter Natishan, Father Gerald Olszewski, Father Jakiw Norton, Father Dragan Filipovic, Father Elias Katras, Father Stevo Rocknage, Father Paul Stoll, Father Igor Soroka, Father Michael Mihalick [MS], Ollie Pendylshok, Walt & Evelyn Burlack, Joshua Agosto and his family, Harley Katarina Rahuba, Mike and Hilda Holupka, Eva Malesnick, Helen Likar, Stella Peanoske, Joe Nezolyk, Nick Behun, Grace Holupka, Virginia Bryan, Joseph Sliwinsky, Maria Balo, Linda Mechtly, Mary Mochnick, Mary Pekich, Mildred Manolovich, Evelyn Misko, Jeanne Boehing, Alex Drobot, Rachelle, Jane Golofski, Doug Diller, Harry Krewsun, Sandy Gamble, Glen Lucas Burlack, Bernie Vangrin, Mary Alice Babcock, Dorie Kunkle, Andrea, & Melissa [Betty O’Masta’s relatives], Mary Evelyn King, Stella Cherepko, Sam Wadrose, Khoruia Joanne Abdalah, Cameron [a boy in Matt’s class], Faith—a 6-year-old girl with rheumatoid arthritis, Isabella Olivia Lindgren—a 2-year-old with a brain tumor, Dillon, Ethel Thomas, Donna, Nick Malec [Maxine’s brother], Erin, Jimmy Fennel [7th Grader], Jim Markovich, Jeff Walewski [thyroid cancer], Carol [Lotinski] Rose, Michael Miller, Dave May, Grace & Owen Ostrasky, Alverta, Margaret Mueller, Gary Zurasky, Michael Horvath, Patti Sinecki, David Genshi, Rita Very & family, Sue Segeleon, Mike Gallagher, Mildred Walters, Michael Miller, Mike Pelchar [Liz’s brother], Jim Logue—throat cancer, Liz Stumpf, Ester Tylavsky, Ed Jamison, Theodore Nixon, Charles Johnson, Amy Forbeck, Michelle Corba Kapeluck, Gloria Prymak [Liz’s niece], Robert Hippert & family, Margaret Vladimir, Luke Emmerling, John Sheliga, Sabrina, George & Mika Rocknage, Elizabeth Mitchell, Amari Clark, Robert McKivitz, Cliff Dow, Marjorie Pershing, Robert Paouncic, and Daria Masur. ARNOLD: Stefania Lucci, Kay Tomson, Ann Ostaffy, Steve Sakal, Homer Paul Kline, and Steve Ostaffy. We pray that God will grant them all a speedy recovery.
Identification of the promoter region and gene expression for human acid alpha glucosidase (1991)

Genetic deficiency of acid alpha glucosidase (GAA) results in glycogen storage disease type II. A cDNA containing the complete coding region was constructed and cloned into the expression vector pSV2 and was transiently transfected into an SV40 immortalized GAA deficient human fibroblast cell line which has undetectable levels of GAA enzyme activity and does not express GAA mRNA. Transfected cells had 4.9% of normal human fibroblast enzyme activity. Additionally a 5' 1.8 kb genomic fragment was ligated to the 5' end of the GAA cDNA construct and cloned into pUC19. Transient and stable transfection also resulted in expressed GAA enzyme activity in deficient fibroblast cells, indicating that the genomic fragment has GAA promoter function.
Supplementary Figure 9 from A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer (2023)

&lt;p&gt;Supplementary Figure 9 shows the Cox proportional hazards model, integrating Moffitt transcriptomic subtype, tumour ploidy, stage and age&lt;/p&gt;