gebhart/patrepeval huggingface dataset:
Population Structure and Evolution of the Bacillus cereus Group (2004)

Representative strains of the Bacillus cereus group of bacteria, including Bacillus anthracis (11 isolates), B. cereus (38 isolates), Bacillus mycoides (1 isolate), Bacillus thuringiensis (53 isolates from 17 serovars), and Bacillus weihenstephanensis (2 isolates) were assigned to 59 sequence types (STs) derived from the nucleotide sequences of seven alleles, glpF, gmk, ilvD, pta, pur, pycA, and tpi. Comparisons of the maximum likelihood (ML) tree of the concatenated sequences with individual gene trees showed more congruence than expected by chance, indicating a generally clonal structure to the population. The STs followed two major lines of descent. Clade 1 comprised B. anthracis strains, numerous B. cereus strains, and rare B. thuringiensis strains, while clade 2 included the majority of the B. thuringiensis strains together with some B. cereus strains. Other species were allocated to a third, heterogeneous clade. The ML trees and split decomposition analysis were used to assign STs to eight lineages within clades 1 and 2. These lineages were defined by bootstrap analysis and by a preponderance of fixed differences over shared polymorphisms among the STs. Lineages were named with reference to existing designations: Anthracis, Cereus I, Cereus II, Cereus III, Kurstaki, Sotto, Thuringiensis, and Tolworthi. Strains from some B. thuringiensis serovars were wholly or largely assigned to a single ST, for example, serovar aizawai isolates were assigned to ST-15, serovar kenyae isolates were assigned to ST-13, and serovar tolworthi isolates were assigned to ST-23, while other serovars, such as serovar canadensis, were genetically heterogeneous. We suggest a revision of the nomenclature in which the lineage and clone are recognized through name and ST designations in accordance with the clonal structure of the population.
Median Effective Dose of Intranasal Dexmedetomidine for Rescue Sedation in Pediatric Patients Undergoing Magnetic Resonance Imaging (2016)

The authors determined the ED50 for rescue sedation using intranasal dexmedetomidine after failed chloral hydrate sedation in children. It was found that ED50 increases with advancing age during the first 3 yr of life.
Recent advances in crystal-induced acute inflammation (2007)

These studies provided a new insight into the mechanisms underlying the initiation and the termination of monosodium urate monohydrate crystal-induced acute inflammation.
Correlation between self-reported recovery and central sensitization in whiplash patients (2012)

Background:Central sensitization has been associated with chronic pain in whiplash patients. Methods:Consecutive whiplash patients were assessed at 3 months post-whiplash injury with the brachial plexus provocation test(BPPT) as a sign of central sensitization.Self-reported recovery was assessed by the response to the question ’Do you feel you have recovered fully from your accident injuries?’ Results:Sixty-nine subjects(32 males,37 females,age 37.5±13.0 years(mean±SD),range 18—71) were included.Of these,34 reported a lack of recovery,and 35 reported recovery at 3 months post-injury.The mean BPPT elbow extension(from 180°) was 41.5±23.0°,and the mean VAS score for the BPPT was 2.2±1.2(out of 10).Those who reported recovery had a mean BPPT elbow extension angle of 25.1±15.8 while those who did not report recovery had a mean BPPT angle of 58.4±15.9(P < 0.05).The visual analogue scale(VAS) score for recovered subjects was 1.8±1.1 and 2.7±1.1(P < 0.05) for non-recovered.There was a moderate correlation between self-reported recovery and BPPT elbow extension angle(—0.44) and a lower correlation between self-reported recovery and VAS score(-0.30). Conclusion:Self-reported recovery correlates well with a lower likelihood of signs of central sensitization.
Perioperative Blood Management Strategies for Total Knee Arthroplasty (2018)

Total knee arthroplasty (TKA) often causes a significant amount of blood loss with an accompanying decline in hemoglobin and may increase the frequency of allogeneic blood transfusion rates. Unfortunately, allogeneic blood transfusions have associated risks including postoperative confusion, infection, cardiac arrhythmia, fluid overload, increased length of hospital stay, and increased mortality. Other than reducing the need for blood transfusions, reducing perioperative blood loss in TKA may also minimize intra-articular hemorrhage, limb swelling, and postoperative pain, and increase the range of motion during the early postoperative period. These benefits improve rehabilitation success and increase patients' postoperative satisfaction. Preoperative anemia, coupled with intraoperative and postoperative blood loss, is a major factor associated with higher rates of blood transfusion in TKA. Thus, treatment of preoperative anemia and prevention of perioperative blood loss are the primary strategies for perioperative blood management in TKA. This review, combined with current evidence, analyzes various methods of blood conservation, including preoperative, intraoperative, and postoperative methods, in terms of their effectiveness, safety, and cost. Because many factors can be controlled to reduce blood loss and transfusion rates in TKA, a highly efficient, safe, and cost-effective blood management strategy can be constructed to eliminate the need for transfusions associated with TKA.
Screening of acrylamide contents in potato crisps using process variable settings and near‐infrared spectroscopy (2006)

In order to study the formation of acrylamide in potato crisps during processing, an experimental design was set up. The design variables were drying time (6 levels), frying temperature (2 levels) and frying time (8 levels). The design contained 36 samples, which were analysed for acrylamide contents using LC high-resolution mass spectroscopy (LC-HRMS), and fat contents using the Soxhlet apparatus. Prior to analysis, all potato crisp samples were ground and analysed on an NIRSystems 6500 near-infrared (NIR) spectrometer. The acrylamide contents were modelled by: (i) design variables using multiple linear regression, (ii) NIR spectra using partial least squares regression (PLSR) and (iii) design variables and NIR spectra in combination using a novel technique combining least squares regression on the former, and PLSR on the latter. The results showed that the NIR spectra alone or in combination with the design variables gave better prediction models for acrylamide than the design variables alone. This implies that the spectra contain chemical information that is not purely a result of the processing variables that were investigated in this experiment. NIR spectroscopy is proposed as a possible tool for screening and identification of potato crisps with a high acrylamide content.
A study on the risk factors of nonalcoholic fatty liver disease in military aircrews (2009)

Objective To analyze the pathogenetic status and risk factors of nonalcoholic fatty liver disease (NAFLD) in military airerews, in order to provide evidence for the treatment and prevention of NAFLD. Methods The study included collecting data as military airerew's age, flying hours and type of aircraft, calculating body mass index (BMI), measuring liver function [alanine transaminase (ALT), aspartase aminotransferase (AST), gamma-glutamyltransferase (GGT)], fasting blood glucose (FBG), uric acid (UA), total cholesterol (TC), triglyceride(TG), high density lipoprotein-cholesterol (HDL-C) and low density lipoprotein-cholesterol (HDL-C), as well as examining liver by B-ultrasound. Results were processed by variance and Logistic regression analysis according to the groups that respectively divided by NAFLD (2 groups), BMI value (2 groups) and ALT value (3 groups by the ranges within ALT<40 U/L, 40 U/L≤ALT<80 U/L and ALT≥ U/L). Results Out of 426 male aircrews, 34.98% were overweight, 19.48% had NAFLD and 16.67% were with high ALT. Compared with normal weight group, morbidity rate of NAFLD and level of ALT were significantly higher than those in over weight group (X2=145.152, 58.959, P< 0.01). Aircrews in ALT≥40 U/L group showed statistical differences on BMI and TG compared to those in ALT<40 U/L group (F=13.476, 13.176, P<0.01). ATL, AST, C, GT, TG, TC, LDL-C, FBG and UA in NAFLD group were significantly higher than those in control group (t= 2.287-7.002, P<0.05 or 0.01), but HDL-C level was significantly lower (t=2.932, P<0.01). There were no statistical differences between fast jet and low speed aircraft (transporter, bomber, helicopter, etc.) aircrews in age, flying hours, BMI and other biochemical indexes. Logistic regression analysis showed that the factors that induced NAFLD were BMI, TG and type of aircraft (Z=37.353, 8.658, 4.486, P<0.05 or 0.01). Conclusions The aircrews have higher morbidity rate of NAFLD with such high risk factors as over weight, high blood lipid (high TG, high LDL-C and low HDLC). So early diagnosis and treatment of NAFLD would be one of the most important measures for limiting its growth and preventing cardiovascular and cerebrovaseular diseases.

Key words: 
Fatty liver;  Alanine transaminase;  Body mass index;  Overweight;  Hyperlipidemias;  Factor analysis, statistical
Shedding of the Lymphocyte L-Selectin Adhesion Molecule Is Inhibited by a Hydroxamic Acid-based Protease Inhibitor (1996)

Expression of the L-selectin adhesion molecule can be rapidly down-modulated by regulated proteolysis at a membrane-proximal site. The L-selectin secretase has remained undefined, and the secretase activity is resistant to a broad panel of common protease inhibitors. We have developed an L-selectin-alkaline phosphatase reporter, consisting of the ectodomain of human placental alkaline phosphatase fused to the membrane-proximal cleavage, transmembrane, and cytoplasmic domains of L-selectin, to aid in the screening for L-selectin secretase inhibitors. A hydroxamic acid-based metalloprotease inhibitor, KD-IX-73-4, inhibited release of the L-selectin-alkaline phosphatase reporter in a dose-dependent manner. The hydroxamic acid-based peptide was also found to inhibit wild type L-selectin down-regulation from the surfaces of phorbol myristate acetate-activated peripheral blood lymphocytes and phytohemagglutinin-stimulated lymphoblasts. Analysis of the proteolytic cleavage fragments of L-selectin confirmed that KD-IX-73-4 inhibited L-selectin proteolysis. Lymphocyte L-selectin was not down-regulated when co-cultured with formylmethionylleucylphenylalanine-stimulated neutrophils, suggesting that the putative secretase acts in cis with the membrane-bound L-selectin. These results suggest that the L-selectin secretase activity may involve a cell surface, zinc-dependent metalloprotease, although L-selectin shedding is not affected by EDTA and may be related to the recently described activity involved in processing of membrane-bound TNF-alpha.
Alzheimers Disease and Retinal Neurodegeneration (2010)

Alzheimer's disease (AD) is the major cause of dementia in the world. Although the entorhinal cortex and hippocampal complex are best known as the sites of early pathology in AD, increasing evidence shows that the eye, particularly the retina, is also affected. The AD-related changes in the retina are associated with degeneration and loss of neurons, reduction of the retinal nerve fibres, increase in optic disc cupping, retinal vascular tortusity and thinning, and visual functional impairment. Given the fact that evaluating pathologic changes in the brain during life has always been an indirect process, largely shielded from view by the barrier of the skull, the eye can be used as a window into diseases of the brain. Using modern techniques, the changes in the retina can be visualized in real-time. In addition to the changes in the eyes of AD patients, similar mechanisms of neurodegeneration in the brain have also been demonstrated in the eye. Targeting AD-liked changes in the retina has been recently shown to be effective in the reduction of retinal neuronal degeneration and loss in eye diseases. This review will cover recent findings on retinal degeneration in AD, pathological similarities between AD and eye diseases, and highlight the potential of modern technologies for the detection of prospective biomarkers in the eye in early AD.
Confirmation of Endotracheal Tube Placement after Intubation Using the Ultrasound Sliding Lung Sign (2006)

These results show that US imaging of the sliding lung sign in a cadaver model is an accurate method for confirmation of ETT placement. Further, the technique may have some utility in differentiating RMS bronchus from main tracheal intubations.
Inertial and magnetic posture tracking for inserting humans into networked virtual environments (2001)

Rigid body orientation can be determined without the aid of a generated source using nine-axis MARG (Magnetic field, Angular Rate, and Gravity) sensor unit containing three orthogonally mounted angular rate sensors, three orthogonal linear accelerometers and three orthogonal magnetometers. This paper describes a quaternion-based complementary filter algorithm for processing the output data from such a sensor. The filter forms the basis for a system designed to determine the posture of an articulated body in real-time. In the system the orientation relative to an Earth-fixed reference frame of each limb segment is individually determined through the use of an attached MARG sensor. The orientations are used to set the posture of an articulated body model. Details of the fabrication of a prototype MARG sensor are presented. Calibration algorithms for the sensors and the human body model are also presented. Experimental results demonstrate the effectiveness of the tracking system and verify the correctness of the underlying theory.
Identification of Conserved Subdominant HIV Type 1 CD8 + T Cell Epitopes Restricted Within Common HLA Supertypes for Therapeutic HIV Type 1 Vaccines (2012)

The high HIV-1 prevalence, up to 4.6% in Guinea-Bissau, West Africa, makes it a relevant location for testing of therapeutic vaccines. With the aim of performing a clinical study in Guinea-Bissau, after first testing the vaccine for safety in Denmark, Europe, we here describe the design of a universal epitope peptide-based T cell vaccine with relevance for any geographic locations. The two major obstacles when designing such a vaccine are the high diversities of the HIV-1 genome and of the human major histocompatibility complex (MHC) class I. We selected 15 CD8-restricted epitopes predicted from conserved regions of HIV-1 that were subdominant (i.e., infrequently targeted) within natural infections. Moreover, the epitopes were predicted to be restricted to at least one of the five common HLA supertypes (HLA-A01, A02, A03, B07, and B44). Here, we validated the resulting peptide-specific, HLA-restricted T cell specificities using peptide-MHC class I tetramer labeling of CD8(+) T cells from HIV-1-infected individuals. The selected vaccine epitopes are infrequently targeted in HIV-1-infected individuals from both locations. Moreover, we HLA-typed HIV-1-infected individuals and demonstrated that the selected vaccine epitopes, when targeted, are restricted to the five most common HLA supertypes at both locations. Thus, the HLA supertype-directed approach achieved HLA coverage of 95% and 100% of the examined cohorts in Guinea-Bissau and Denmark, respectively. In conclusion, the selected vaccine epitopes match the host populations and HIV-1 strains of these two distant geographic regions, justifying clinical testing in both locations.
Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships (2015)

Neural networks were widely used for quantitative structure-activity relationships (QSAR) in the 1990s. Because of various practical issues (e.g., slow on large problems, difficult to train, prone to overfitting, etc.), they were superseded by more robust methods like support vector machine (SVM) and random forest (RF), which arose in the early 2000s. The last 10 years has witnessed a revival of neural networks in the machine learning community thanks to new methods for preventing overfitting, more efficient training algorithms, and advancements in computer hardware. In particular, deep neural nets (DNNs), i.e. neural nets with more than one hidden layer, have found great successes in many applications, such as computer vision and natural language processing. Here we show that DNNs can routinely make better prospective predictions than RF on a set of large diverse QSAR data sets that are taken from Merck's drug discovery effort. The number of adjustable parameters needed for DNNs is fairly large, but our results show that it is not necessary to optimize them for individual data sets, and a single set of recommended parameters can achieve better performance than RF for most of the data sets we studied. The usefulness of the parameters is demonstrated on additional data sets not used in the calibration. Although training DNNs is still computationally intensive, using graphical processing units (GPUs) can make this issue manageable.
Fabrication of 3D hepatic tissues by additive photopatterning of cellular hydrogels (2006)

We have fabricated a hepatic tissue construct using a multilayer photopatterning platform for embedding cells in hydrogels of complex architecture. We first explored the potential of established hepatocyte culture models to stabilize isolated hepatocytes for photoencapsulation (e.g., double gel, Matrigel, cocultivation with nonparenchymal cells). Using photopolymerizable PEG hydrogels, we then tailored both the chemistry and architecture of the hydrogels to further support hepatocyte survival and liver-specific function. Specifically, we incorporated adhesive peptides to ligate key integrins on these adhesion-dependent cells. To identify the appropriate peptides for incorporation, the integrin expression of cultured hepatocytes was monitored by flow cytometry and their functional role in cell adhesion was assessed on full-length extracellular matrix (ECM) molecules and their adhesive peptide domains. In addition, we modified the hydrogel architecture to minimize barriers to nutrient transport for these highly metabolic cells. Viability of encapsulated cells was improved in photopatterned hydrogels with structural features of 500 microm in width over unpatterned, bulk hydrogels. Based on these findings, we fabricated a multilayer photopatterned PEG hydrogel structure containing the adhesive RGD peptide sequence to ligate the alpha5beta1 integrin of cocultured hepatocytes. Three-dimensional photopatterned constructs were visualized by digital volumetric imaging and cultured in a continuous flow bioreactor for 12 d where they performed favorably in comparison to unpatterned, unperfused constructs. These studies will have impact in the field of liver biology as well as provide enabling tools for tissue engineering of other organs.
Wide dynamic range detection of bidirectional flow in Doppler optical coherence tomography using a two-dimensional Kasai estimator (2007)

We demonstrate extended axial flow velocity detection range in a time-domain Doppler optical coherence tomography (DOCT) system using a modified Kasai velocity estimator with computations in both the axial and transverse directions. For a DOCT system with an 8 kHz rapid-scanning optical delay line, bidirectional flow experiments showed a maximum detectable speed of >56 cm/s using the axial Kasai estimator without the occurrence of aliasing, while the transverse Kasai estimator preserved the approximately 7 microm/s minimum detectable velocity to slow flow. By using a combination of transverse Kasai and axial Kasai estimators, the velocity detection dynamic range was over 100 dB. Through a fiber-optic endoscopic catheter, in vivoM-mode transesophageal imaging of the pulsatile blood flow in rat aorta was demonstrated, for what is for the first time to our knowledge, with measured peak systolic blood flow velocity of >1 m/s, while maintaining good sensitivity to detect aortic wall motion at <2 mm/s, using this 2D Kasai technique.
Case 41-1985 (1985)

Presentation of CaseAn 84-year-old woman was admitted to the hospital because of bloody diarrhea.She was in a stable state of health until three weeks earlier, when diarrhea developed, with the daily passage of 10 to 12 purulent, blood-streaked stools of small volume, particularly after eating. Her undergarments were sometimes stained with feces, especially when she arose from her bed. Constant pain appeared in the left lower abdominal quadrant. On the day of admission a neighbor reported her condition to her physician, and she was admitted to the hospital.The patient was widowed 10 years before admission. She lived . . .
Quantification of plasma cell-free DNA in patients with gastric cancer. (2007)

The plasma DNA concentration assay may serve as a new diagnostic marker for the screening and monitoring of patients with gastric cancer.
Purification and characterization of N‐acetylglucosamine kinase from rat liver (1998)

N-Acetylglucosamine, a major sugar in complex carbohydrates, enters the pathways of aminosugar metabolism by the action of N-acetylglucosamine kinase (EC 2.7.1.59). In this study we report the purification to homogeneity of GlcNAc kinase from rat liver cytosol using salmine sulfate precipitation, chromatography on phenyl-Sepharose, ATP-agarose and MonoQ, and finally gel filtration on Superdex 200. It was characterized as a dimer of 39-kDa subunits. About 25% of the amino acid sequence of GlcNAc kinase was established by peptide mapping. Part of the ATP-binding site of GlcNAc kinase was identified by sequence comparison with related hexokinases, including the bifunctional enzyme UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (EC 5.1.3.14/2.7.1.60), the key enzyme of N-acetylneuraminic acid biosynthesis in rat liver. The Cys residues in the active sites of GlcNAc kinase and ManNAc kinase were characterized by chemical modification with N-ethylmaleimide, iodoacetamide and 5,5'-dithiobis(2-nitrobenzoic acid). The finding that the substrates GlcNAc and ManNAc protected their respective enzymes from inhibition by the above sulfhydryl reagents indicates that Cys residues are located in or near the active sites of both enzymes. Use of the specific dithiol-modifying chemical reagents, sodium meta-periodate, sodium meta-arsenite/2,3-dimercaptopropanol and diazenedicarboxylic acid bis-N,N'-dimethylamide revealed that the active sites of GlcNAc kinase and ManNAc kinase possess at least one pair of vicinal thiols. Chemical treatment of UDP-GlcNAc 2-epimerase provided no evidence for the presence of cysteine in the active site of this enzyme. From the incorporation of N-[3H]ethylmaleimide into GlcNAc kinase in the absence and presence of ligands we estimated that the active site of GlcNAc kinase contains two Cys residues.
Evaluation of the contingent replication assay (CRA) and its application to the study of the general transcription initiation factor, TFIIF (1993)

The Contingent replication assay (CRA) is a rapid assay for the screening and isolation of cDNAs by protein-protein or protein-DNA interactions in mammalian cells. The method has been shown to enrich a plasmid containing a cDNA encoding the bacterial replication-related protein, R6K, from a mixture of two plasmids. In this report we present data illustrating the sensitivity and selectivity of the method. Using the small subunit of TFIIF (Rap30) as a target, we demonstrate the enrichment of a clone encoding the large subunit, Rap74, from a cDNA library. Additional cDNA clones including human Rap30 and an anonymous cDNA clone homologous to members of the human cdc2 kinase family were enriched and isolated by a modified screening approach. The structure of these additional clones suggest that the CRA enriches for products that interact not only directly with the target protein but also through bridging by endogenous proteins.