gebhart/patrepeval huggingface dataset:
Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control (1989)

Mutations at the Escherichia coli pcnB locus reduce the copy number of ColE1-like plasmids. We isolated additional mutations in this gene and conducted a preliminary characterization of its product. F-prime elements carrying the pcnB region were constructed and used to show that the mutations were recessive. The wild-type pcnB gene was cloned into a low-copy-number plasmid, and its nucleotide sequence was determined. The sequence analysis indicated that pcnB is probably the first gene in an operon that contains one or more additional genes of unknown function. The pcnB locus should encode a polypeptide of 47,349 daltons (Da). A protein of this size was observed in minicells carrying a pcnB+ plasmid, and transposon insertions and deletions that truncated this protein generally abolished pcnB function. One exceptional transposon insertion at the promoter-distal end of the pcnB gene truncated the 47-kDa protein by about 20% but did not abolish complementation activity, indicating that the C-terminus of the PcnB product is dispensable. The deduced amino acid sequence of PcnB revealed numerous charged residues and, with 10% arginines, an overall basic character, suggesting that PcnB might interact with DNA or RNA in a structural capacity. Disruption of the pcnB gene by insertional mutagenesis caused a reduction in growth rate, indicating that PcnB has an important cellular function.
Three-dimensional computational holographic imaging and recognition using independent component analysis (2007)

We present computational holographic three-dimensional imaging and automated object recognition based on independent component analysis (ICA). Three-dimensional sensing of the scene is performed by computational holographic imaging of the objects using phase-shifting digital holography. We used principal components analysis to reduce data dimension and ICA to recognize the three-dimensional objects. In this paper, kurtosis maximization-based algorithm is used. To the best of our knowledge, this paper is the first to report using ICA in three-dimensional imaging technology.
SAR micromotion target detection based on gapped sine curves (2012)

This paper presents a detection algorithm for micromotion targets, such as rotating antennas, in the synthetic aperture radar (SAR) geometry. It utilizes target's range cell migration characteristics, i.e. a micromotion target takes on a sine cure in the slowtime-range image, but with incontinuity or gaps when clutter (and part of target energy) is suppressed. Two-stage detection, including MTI and the extended Hough transform, is used to suppress clutter and to extract the sine curve. Quasi-real SAR data of Isleta Lake demonstrate high SNR gains and good detection performance.
The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung consolidation (2018)

Preweaning is a high-risk time period for dairy calves; pneumonia is a predominant cause of mortality and use of antibiotics on farms. Given the concern of antibiotic resistance, there is demand to investigate alternative therapies. Administering probiotics to alter the respiratory microbiome and reduce the risk of pneumonia has shown promising results in mice. Although the bacterial community dynamics of the upper airway have been investigated in dairy calves, they have not been evaluated in calves diagnosed with pneumonia using lung ultrasound (US). By allowing visualization of lung consolidation, US increases the sensitivity of pneumonia diagnosis. Elucidating phenotypes of the commensal community in healthy and pneumonic dairy calves is crucial to investigating probiotics as a preventative for pneumonia. The primary objective of this prospective case-control study was to describe bacterial communities in the nasopharynx (NP) of preweaned dairy calves with and without lung consolidation. Secondary objectives included evaluating the effects of previous antibiotic therapy and age on the composition of NP microbiota.
<title>Time frequency and chirps</title> (2001)

Chirps (i.e., transient AM-FM waveforms) are ubiquitous in nature and man-made systems, and they may serve as a paradigm for many nonstationary deterministic signals. The time-frequency plane is a natural representation space for chirps, and we will here review a number of questions related to chirps, as addressed from a time-frequency perspective. Global and local approaches will be described for matching and/or adapting representations to chirps. As a corollary, joint time-frequency descriptions of chirps will be shown to allow for effective definitions of instantaneous frequencies via localized trajectories on the plane. A number of applications will be mentioned, ranging from bioacoustics to turbulence and gravitational waves.
Testing Hypotheses of Functional Structure: Some Rules for Determining Flexibility of Restricted Production Models (1992)

Abstract Rules are proposed to help determine whether a production function maintains flexibility under parametric restrictions required to impose homogeneity, homotheticity, and forms of separability. After imposing restrictions and applying the rules, many second‐order “flexible” forms are found to be more inflexible than formerly believed.
Quality Controlled Paraphrase Generation (2022)

Paraphrase generation has been widely used in various downstream tasks. Most tasks benefit mainly from high quality paraphrases, namely those that are semantically similar to, yet linguistically diverse from, the original sentence. Generating high-quality paraphrases is challenging as it becomes increasingly hard to preserve meaning as linguistic diversity increases. Recent works achieve nice results by controlling specific aspects of the paraphrase, such as its syntactic tree. However, they do not allow to directly control the quality of the generated paraphrase, and suffer from low flexibility and scalability. Here we propose $QCPG$, a quality-guided controlled paraphrase generation model, that allows directly controlling the quality dimensions. Furthermore, we suggest a method that given a sentence, identifies points in the quality control space that are expected to yield optimal generated paraphrases. We show that our method is able to generate paraphrases which maintain the original meaning while achieving higher diversity than the uncontrolled baseline. The models, the code, and the data can be found in https://github.com/IBM/quality-controlled-paraphrase-generation.
Hepatocellular Carcinoma Detection by Gallium Scan and Subsequent Treatment by Gallium Maltolate: Rationale and Case Study (2011)

Gallium is antiproliferative to many types of cancer, due primarily to its ability to act as a non-functional mimic of ferric iron (Fe(3+)). Because Fe(3+) is needed for ribonucleotide reductase activity--and thus DNA synthesis--gallium can inhibit DNA production and cell division. Diagnostic gallium scans have shown that hepatocellular carcinoma (HCC) is commonly avid for gallium. Furthermore, in vitro studies have found that gallium nitrate, and particularly gallium maltolate (GaM), have dose-dependent antiproliferative activity against HCC cell lines. Rationale thus exists to use GaM, an orally active compound that has been well tolerated in Phase I clinical trials, to treat patients whose HCC is gallium-avid in a gallium scan. Because gallium absorbed from orally administered GaM is bound predominately to serum transferrin, which travels to all tissues in the body, GaM has the potential to treat even distant metastases. A patient with advanced HCC (20 × 10 cm primary tumor, ascites around liver and spleen, resistant to Nexavar(®) (sorafenib)), whose cancer was highly gallium-avid in a (67)Ga-scan, was treated with oral gallium maltolate at 1500 mg/day q.d. After four weeks of treatment, the patient had a large reduction in pain, with greatly increased mobility and quality of life, and significantly lowered serum bilirubin and inflammation-related liver enzymes. At eight weeks, CT scans showed apparent necrosis of the tumor.
Impact of screening on cervical cancer incidence: A population‐based case–control study in the United States (2019)

Cervical cancer is widely preventable through screening, but little is known about the duration of protection offered by a negative screen in North America. A case-control study was conducted with records from population-based registries in New Mexico. Cases were women diagnosed with cervical cancer in 2006-2016, obtained from the Tumor Registry. Five controls per case from the New Mexico HPV Pap Registry were matched to cases by sex, age and place of residence. Dates and results of all cervical screening and diagnostic tests since 2006 were identified from the pap registry. We estimated the odds ratio of nonlocalized (Stage II+) and localized (Stage I) cervical cancer associated with attending screening in the 3 years prior to case-diagnosis compared to women not screened in 5 years. Of 876 cases, 527 were aged 25-64 years with ≥3 years of potential screening data. Only 38% of cases and 61% of controls attended screening in a 3-year period. Women screened in the 3 years prior to diagnosis had 83% lower risk of nonlocalized cancer (odds ratio [OR] = 0.17, 95% CI: 0.12-0.24) and 48% lower odds of localized cancer (OR = 0.52, 95% CI: 0.38-0.72), compared to women not screened in the 5 years prior to diagnosis. Women remained at low risk of nonlocalized cancer for 3.5-5 years after a negative screen compared to women with no negative screens in the 5 years prior to diagnosis. Routine cervical screening is effective at preventing localized and nonlocalized cervical cancers; 3 yearly screening prevents 83% of nonlocalized cancers, with no additional benefit of more frequent screening. Increasing screening coverage remains essential to further reduce cervical cancer incidence.
Porcine Babesiosis Caused by Babesia sp. Suis in a Pot-Bellied Pig in South Africa (2021)

Babesiosis is a worldwide, tick-borne disease of economic importance in livestock caused by <i>Babesia</i> spp., which are hemoparasitic piroplasms that target the host erythrocytes. Cattle, dogs, small ruminants, and wild ruminants are the species most commonly affected, while in cats, horses, and pigs, it is less frequently reported. Although babesiosis has been observed worldwide, porcine babesiosis remains an uncommon disease with a very limited number of cases reported. Here, we describe a case in a 12-year old pot-bellied pig from South Africa that died after a history of anorexia and reluctance to rise for 2 days. A complete necropsy, blood smear cytology, reverse line blot (RLB) hybridization and 18S rRNA sequencing were performed. Numerous <i>Babesia</i> spp. hemoparasites and a moderate regenerative anemia were identified on blood smear, and a urine dipstick test yielded 4+ heme. Diffuse icterus and splenomegaly were observed upon gross examination. Histopathology revealed hemoglobin casts within renal tubules and collecting ducts, pulmonary edema, splenic congestion, and intrahepatic cholestasis. BLASTN homology of the 18SrRNA sequence revealed a 100% identity to the published sequence of <i>Babesia</i> sp. Suis isolated from pigs in Italy. This case of babesiosis in a pig highlights the clinical manifestations and gross and pathological findings of porcine babesiosis.
Process parameter influence to negative tone development process for double patterning (2010)

Process parameter influence in resist process with negative tone development (NTD) to pattern size (CD), CD uniformity (CUD), and defectivity are studied to estimate the impact for process stability in high volume manufacturing (HVM) of semiconductor devices. Since double exposure process is one of the candidates in contact hole patterning, exposure to exposure delay was studied. There is a possibility to design the off-line system with NTD process, therefore, exposure - PEB delay and PEB - development delay were studied. As basic development parameter studies, development time, developer temperature, developer volume, and rinse time dependency on CD, CDU, and defectivity were investigated.
Transformation of spin information into large electrical signals via carbon nanotubes (2005)

Spin electronics (spintronics) exploits the magnetic nature of the electron, and is commercially exploited in the spin valves of disc-drive read heads. There is currently widespread interest in using industrially relevant semiconductors in new types of spintronic devices based on the manipulation of spins injected into a semiconducting channel between a spin-polarized source and drain. However, the transformation of spin information into large electrical signals is limited by spin relaxation such that the magnetoresistive signals are below 1%. We overcome this long standing problem in spintronics by demonstrating large magnetoresistance effects of 61% at 5 K in devices where the non-magnetic channel is a multiwall carbon nanotube that spans a 1.5 micron gap between epitaxial electrodes of the highly spin polarized manganite La0.7Sr0.3MnO3. This improvement arises because the spin lifetime in nanotubes is long due the small spin-orbit coupling of carbon, because the high nanotube Fermi velocity permits the carrier dwell time to not significantly exceed this spin lifetime, because the manganite remains highly spin polarized up to the manganite-nanotube interface, and because the interfacial barrier is of an appropriate height. We support these latter statements regarding the interface using density functional theory calculations. The success of our experiments with such chemically and geometrically different materials should inspire adventure in materials selection for some future spintronics
Epidemiological survey of acute low-tone sensorineural hearing loss (2017)

The severity of initial hearing loss, interval between onset and initial visit and age were important prognostic indicators for ALHL, while female gender was an important prognostic indicator peculiar to ALHL.
The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment (2013)

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.
Instabilities and phase transitions in human brain and behavior (2010)

GENERAL COMMENTARY article Front. Hum. Neurosci., 11 March 2010Sec. Cognitive Neuroscience https://doi.org/10.3389/fnhum.2010.00023
CCR2 (chemokine (C-C motif) receptor 2) (2012)

Review on CCR2 (chemokine (C-C motif) receptor 2), with data on DNA, on the protein encoded, and where the gene is implicated.
How to Interpret Borderline HCV Antibody Test Results: A Comparative Study Investigating Four Different Anti-HCV Assays (2014)

Anti-HCV testing is the first step to diagnose hepatitis C. Although anti-HCV assay performance improved during the last 2 decades, very high sensitivity required for screening may lead to limitations in specificity. Thus, there remains an uncertainty how to interpret anti-HCV test results with a borderline signal-to-cut-off ratio. Comparison was made of concordance and performance of four licensed anti-HCV assays in samples with borderline signal-to-cut-off ratios. Out of 12,090 consecutive samples tested for anti-HCV with the Abbott Architect Anti-HCV assay over a period of 29 months, 95 plasma samples with a signal-to-cut-off ratio between 0.5 and 2 were selected for this study. All samples were re-tested with the Enzygnost Anti-HCV version 4.0, the Ortho anti-HCV version 3.0, and the Monolisa anti-HCV-Plus version 2 assays. Discordant samples were classified by additional immunoblot testing. Overall, only 52% of the Architect borderline samples gave similar results in all four assays. Inter-assay concordance ranged between 58% and 80%. The highest discordance was observed between the Architect and the Monolisa assay (42%). In contrast, a high level of concordance was found between the Enzygnost and Ortho assays (80%). The Monolisa was best to identify negative samples (100%), while the Enzygnost correctly classified most of the positive samples (96%). Anti-HCV antibody assays show significant variation in classifying samples with low signal-to-cut-off ratios. Different performances may have cost and management implications, as false-positive results are not infrequent. However, sensitivities were good for all assays if indeterminate results are not considered as negative.
Missile Controlled by Lift and Divert Thrusters Using Nonlinear Dynamic Sliding Manifolds (2006)

A new approach to the design of a kinetic-kill longitudinal autopilot steering the missile trajectory by the combination of aerodynamic lift and divert thrusters (dual-thrusters control) and with its attitude oriented by attitude thrusters is presented. The proposed approach may increase the total divert acceleration capability by up to 100%, improving the end-game intercept accuracy, when such capability is required. The pitch plane autopilot design is based on second-order sliding mode control using a nonlinear dynamic sliding manifold technique. A robust high-accuracy tracking of the missile normal acceleration guidance command is achieved in the presence of considerable model uncertainties created by the interactions between the airflow and the thrusters jets. Results of the computer simulation demonstrate excellent, robust, high-accuracy tracking performance of the proposed design.
AN INVESTIGATION OF 3-D CURLED CHIP IN MACHINING-PART 1: A MECHANICS-BASED ANALYTICAL MODEL (1998)

Abstract This paper presents an analytical model of the 3-D curled chip that is commonly produced in oblique machining. The chip model is based on a 3-D spiral with continuously varying center and curl radius. Stresses in the chip are analyzed by an energy-based approach. Bending and torsional shear stresses in the chip are generated based on input reaction forces. A case study with typical input values of reaction forces is analyzed for finding the magnitude and location of the maximum stresses. Also, the octahedral shear stress is proposed as a comprehensive 3-D chip failure criterion, because it combines the individual effects of the bending and shear stresses.
Relationship Between Levels of Very Virulent MDV in Poultry Dust and in Feather Tips from Vaccinated Chickens (2013)

To assess the effect of various vaccine strains on replication and shedding of virulent Marek's disease virus from experimentally infected chickens, quantitative PCR (q-PCR) methods were developed to accurately quantify viral DNA in infected chickens and in the environment in which they were housed. Four groups of 10 chickens, kept in poultry isolators, were vaccinated at 1 day old with one of four vaccines covering each of the three vaccine serotypes, then challenged with very virulent MDV strain Md5 at 8 days of age. At regular time-points, feather tips were collected from each chicken and poultry dust was collected from the air-extract prefilter of each isolator. DNA was extracted from feather and dust samples and subjected to real-time q-PCR, targeting the U(S)2 gene of MDV-1, in order to measure Md5 level per 10(4) feather tip cells or per microgram of dust. Accuracy of DNA extraction from dust and real-time q-PCR were validated by comparing either q-PCR cycle threshold values or the calculated MDV genome level; for use in q-PCR, DNA was extracted from serial dilutions of MDV-infected dust diluted with noninfected dust, or DNA from MDV-infected dust was diluted with DNA from noninfected dust. The results confirmed the accuracy and sensitivity of dust DNA extraction and subsequent q-PCR and showed that differences in virus levels between dust samples truly reflect differences in shedding. Vaccination delayed both replication of Md5 in feather tips and shedding of Md5. First detection of Md5 in feather tips always preceded or coincided with first detection in dust in each group. pCVI988 and HVT+SB-1 were the most efficient vaccines in reducing both replication and shedding of Md5. There was close correlation between mean virus level in feathers of each group and mean virus level in the dust shed by that group. This relationship was similar in each of the vaccinated groups, demonstrating that measurement of the virus in dust can be used to monitor accurately both the infection status of the chickens and environmental contamination by MDV.
Generation of 1 mJ, 85 fs, 2.5 μm Pulses from a Cr 2+ :ZnSe Chirped Pulse Amplifier (2018)

We demonstrate the generation of 1 mJ, 85 fs, 2.5 µm pulses with 300 nm of available bandwidth at 1 kHz of repetition rate from a Chirped Pulse Amplifier based on the Cr2+: ZnSe gain medium.
ChemInform Abstract: Redox Properties of Diaryl Chalcogenides and Their Oxides (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Evaluation and Application of the Transient-Pulse Technique for Determining the Hydraulic Properties of Low-Permeability Rocks—Part 2: Experimental Application (2000)

Abstract In Part 1 of this study, the general solution to the transient-pulse test (Hsieh et al. 1981) was extended to evaluate quantitatively the transient variations in hydraulic head and the corresponding distributions of hydraulic gradient within a test specimen. In addition, the conditions and the validity of using the expression proposed by Brace et al. (1968) to compute the low permeability of a rock specimen from a transient-pulse test were examined. Some theoretical considerations related to the optimal design of a transient-pulse test were also discussed. Part 2 presents a relatively general and convenient approach for determining not only the hydraulic conductivity and specific storage of a specimen directly from a transient-pulse test, but also the compressive storage of the fluid reservoirs. The accuracy and efficiency of this method are demonstrated through (1) the comparison of the compressibility of the fluid-reservoir (permeating) system back-calculated from the transient-pulse tests with the value obtained from calibration tests, and (2) its application to a series of experimental studies designed to investigate the effects of confining pressure on the hydraulic properties of Shirahama sandstone and Inada granite, two rock types available widely in Japan.
Outcome in prostate cancer: association with endothelial nitric oxide synthase Glu-Asp298 polymorphism at exon 7. (2002)

This study demonstrates a strong association between Glu-Asp298-GG genotype as a nitric oxide-related genetic factor and advanced disease and bone metastasization. The establishment of a genetic profile for each patient may be useful in the prediction of the outcome of prostate cancer patients.