gebhart/patrepeval huggingface dataset:
A Phosphonate-Induced Gene Which Promotes <i>Penicillium</i> -Mediated Bioconversion of <i>cis</i> -Propenylphosphonic Acid to Fosfomycin (1999)

Penicillium decumbens is able to epoxidize cis-propenylphosphonic acid (cPA) to produce the antibiotic fosfomycin [FOM; also referred to as phosphonomycin and (-)-cis-1,2-epoxypropylphosphonic acid], a bioconversion of considerable commercial significance. We sought to improve the efficiency of the process by overexpression of the genes involved. A conventional approach of isolating the presumed epoxidase and its corresponding gene was not possible since cPA epoxidation could not be achieved with protein extracts. As an alternative approach, proteins induced by cPA were detected by two-dimensional gel electrophoresis. The observation that a 31-kDa protein (EpoA) was both cPA induced and overaccumulated in a strain which more efficiently converted cPA suggested that it might take part in the bioconversion. EpoA was purified, its amino acid sequence was partially determined, and the corresponding gene was isolated from cosmid and cDNA libraries with oligonucleotide probes. The DNA sequence for this gene (epoA) contained two introns and an open reading frame encoding a peptide of 277 amino acids having some similarity to oxygenases. When the gene was subcloned into P. decumbens, a fourfold increase in epoxidation activity was achieved. epoA-disruption mutants which were obtained by homologous recombination could not convert cPA to FOM. To investigate the regulation of the epoA promoter, the bialaphos resistance gene (bar, encoding phosphinothricin acetyltransferase) was used to replace the epoA-coding region. In P. decumbens, expression of the bar reporter gene was induced by cPA, FOM, and phosphorous acid but not by phosphoric acid.
Kinetic Characterization of Native and Cysteine 112-Modified Glutathione <i>S</i>-Transferase A1-1:  Reassessment of Nonsubstrate Ligand Binding (2002)

We have prepared human glutathione S-transferase isoform A1-1 (GST A1-1) which has been chemically modified at cysteine 112. These modifications include formation of mixed disulfides with glutathione ("glutathiolation") and cross-linkage of the GST dimer with bis-maleimides reacting with the equivalent Cys 112 residues of the two monomers. This residue (Cys 112) lies adjacent to the hydrophobic substrate binding site, and its side chain thiol projects into the large, solvent-filled cleft which is widely reported in the literature to be the binding site of nonsubstrate ligands. Both types of modification block this intersubunit cleft region and significantly change its chemical environment. Kinetic experiments with these altered enzymes revealed that neither type of modification affects the catalytic activity of GST A1-1 or the binding of nonsubstrate ligands. The lack of an effect on glutathione conjugation activity is somewhat surprising given the proximity of cysteine 112 to the hydrophobic substrate binding site. More surprising, however, is the observation that modification at cysteine 112 has no effect on the binding of nonsubstrate ligands. Furthermore, two of these ligands, lithocholic acid and estradiol disulfate, unexpectedly exhibited competitive inhibition of the unmodified enzyme, suggesting that they bind in the hydrophobic substrate site rather than some accessory ligand binding site. Together, these results strongly argue against the intersubunit cleft as the nonsubstrate ligand binding site and prompt a reassessment of how these ligands interact with GST A1-1.
Investigation of KIT gene mutations in women with 46,XX spontaneous premature ovarian failure (2002)

BACKGROUND: Spontaneous premature ovarian failure presents most commonly with secondary amenorrhea. Young women with the disorder are infertile and experience the symptoms and sequelae of estrogen deficiency. The mechanisms that give rise to spontaneous premature ovarian failure are largely unknown, but many reports suggest a genetic mechanism in some cases. The small family size associated with infertility makes genetic linkage analysis studies extremely difficult. Another approach that has proven successful has been to examine candidate genes based on known genetic phenotypes in other species. Studies in mice have demonstrated that c-kit, a transmembrane tyrosine kinase receptor, plays a critical role in gametogenesis. Here we test the hypothesis that human KIT mutations might be a cause of spontaneous premature ovarian failure. METHODS AND RESULTS: We examined 42 women with spontaneous premature ovarian failure and found partial X monosomy in two of them. In the remaining 40 women with known 46,XX spontaneous premature ovarian failure we evaluated the entire coding region of the KIT gene. We did this using polymerase chain reaction based single-stranded conformational polymorphism analysis and DNA sequencing. We did not identify a single mutation that would alter the amino acid sequence of the c-KIT protein in any of 40 patients (upper 95% confidence limit is 7.2%). We found one silent mutation at codon 798 and two intronic polymorphisms. CONCLUSION: Mutations in the coding regions of the KIT gene appear not to be a common cause of 46,XX spontaneous premature ovarian failure in North American women.
Cognitive and motor development during childhood in boys with Klinefelter syndrome (2008)

The goal of this study was to expand the description of the cognitive development phenotype in boys with Klinefelter syndrome (47,XXY). We tested neuropsychological measures of memory, attention, visual-spatial abilities, visual-motor skills, and language. We examined the influence of age, handedness, genetic aspects (parental origin of the extra X chromosome, CAG(n) repeat length, and pattern of X inactivation), and previous testosterone treatment on cognition. We studied 50 boys with KS (4.1-17.8 years). There was a significant increase in left-handedness (P = 0.002). Specific language, academic, attentional, and motor abilities tended to be impaired. In the language domain, there was relative sparing of vocabulary and meaningful language understanding abilities but impairment of higher level linguistic competence. KS boys demonstrated an array of motor difficulties, especially in strength and running speed. Deficits in the ability to sustain attention without impulsivity were present in the younger boys. Neither genetic factors examined nor previous testosterone treatment accounted for variation in the cognitive phenotype in KS. The cognitive results from this large KS cohort may be related to atypical brain lateralization and have important diagnostic and psychoeducational implications. The difficulty in complex language processing, impaired attention and motor function in boys with KS may be missed. It is critical that boys with KS are provided with appropriate educational support that targets their learning challenges in school in addition to modifications that address their particular learning style. These findings would also be an important component of counseling clinicians and families about this disorder.
Video-assisted thoracoscopic surgery for closure of patent ductus arteriosus in children. (1997)

Video-assisted thoracoscopic surgery (VATS) was recently described as an approach to clip the patent ductus arteriosus (PDA). Between May 1994 and May 1996, we performed this procedure on 34 children below 12 years of age (mean 7 years). Thirty-two had an isolated PDA and two had associated small perimembranous ventricular septal defect (VSD), diagnosed on echocardiography and colour flow mapping. None had pulmonary arterial hypertension. The procedure was successful in 33 (97%) children confirmed by absence of residual shunt on serial echocardiography. Complications in the form of pneumothorax (1) and vocal card paralysis (2) were encountered in three children. The overall hospital stay was reduced to five days. In conclusion, the technique of PDA clipping using VATS is easy to learn and highly successful with acceptable risk of complications.
The Impact of a GenCyber Camp on In-service Teachers’ TPACK (2023)

The purpose of this study was to examine the impact of a GenCyber camp curriculum on teachers’ technology, pedagogy, and content knowledge (TPACK). The camp was designed to engage participants in developing the knowledge and skills to incorporate GenCyber Cybersecurity First Principles and GenCyber Cybersecurity Concepts (GenCyber, 2019) into their curriculums. Participants (37 middle and high school teachers from a variety of disciplines) attended one of two weeklong camps held at a Midwestern liberal arts university. Using the TPACK Self-Reflection and TPACK Self-Assessment Surveys, pre- and post-camp data were collected from participants. Findings indicate that participants demonstrated an increase in all domains of the TPACK framework from pre- to post-survey. The greatest increase was in Technological Pedagogy Knowledge (TPK) (0.57), followed by Pedagogical Content Knowledge (PCK) (0.51), and Technological Pedagogical Content Knowledge (TPACK) (0.46). GenCyber participants also demonstrated an average increase in pre- and post-test scores in all areas on the TPACK Self-Assessment Survey Results; however, individual results were mixed. The majority of participants (n=21), sixty percent, saw an increase in composite score from pre- to post, whereas 12 participants' (34%) scores decreased from pre- to post, and two (6%) stayed the same. Findings indicate the GenCyber Camp provided in-service teachers with the knowledge and skills necessary to incorporate GenCyber Principles and Cybersecurity Concepts into their curriculum. Recommendations for teacher professional development on cybersecurity are made.
Total Synthesis of Lehualide B by Allylic Alcohol−Alkyne Reductive Cross-Coupling (2010)

The total synthesis of anticancer marine natural product lehualide B is described. Overall, the synthesis proceeds in just eight steps from a simple gamma-pyrone, does not require the use of protecting groups, and delivers each nonconjugated trisubstituted alkene with high levels of stereoselection. The challenging C12-C16 bis-trisubstituted 1,4-diene was installed with a complex reductive cross-coupling reaction between a preformed Ti-alkyne complex and a pyrone-containing allylic alcohol.
A108 PROBIOTICS FOR CELIAC DISEASE: A SYSTEMATIC REVIEW AND META-ANALYSIS OF RANDOMIZED CONTROLLED TRIALS (2020)

Abstract Background Celiac disease is a chronic autoimmune disorder triggered by dietary gluten. The only available treatment for celiac disease is strict compliance to the gluten-free diet. Despite adherence to a gluten-free diet, many celiac patients still experience symptoms which may be mediated by the gut microbiota. Different studies have assessed the use of probiotics as an adjuvant treatment for celiac disease. Aims We performed a systematic review and meta-analysis to evaluate the efficacy of probiotics in improving gastrointestinal symptoms and quality of life in patients with celiac disease. Methods We searched MEDLINE (1966 to February 2019), EMBASE (1974 to February 2019), CINAHL, Web of Science, CENTRAL, DARE, and Sigle up to February 2019 for randomized controlled trials (RCTs) assessing the effects of probiotics on celiac disease. We collected data on gastrointestinal symptoms, quality of life, adverse events, serum tumor necrosis factor α (TNF-α), intestinal permeability, and microbiota composition. Results Out of 2831 records screened, 7 articles from 6 RCTs with a total of 279 participants were eligible for quantitative analysis. Probiotic supplementation for a minimum of 2 weeks improved gastrointestinal symptoms when assessed by the Gastrointestinal Symptoms Rating Scale (GSRS) (2 studies; 131 participants; mean difference (MD) symptom reduction: -28.7%; 95% CI -43.96 to -13.52; P=0.0002). No differences in gastrointestinal symptoms after probiotics were observed when pooling data from the GSRS, Celiac Symptoms Index (CSI), and the Celiac Disease Questionnaire (CDQ) (4 studies; 197 participants; standardized mean difference (SMD) symptom reduction: -0.48; 95% CI -1.21 to +0.25; P=0.20). TNF-α levels did not change after probiotics (SMD: -0.52; 95% CI -1.08 to +0.04; P=0.07). Levels of Bifidobacteria species increased (MD: increase by 0.85 log CFU/g; 95% CI +0.38 to +1.32 log CFU/g; P=0.0003) but there was no difference in Lactobacilli species (MD: change of 1.13 log CFU/g; 95% CI -0.67 to +2.93 log CFU/g; P=0.22) after probiotic supplementation. No difference in quality of life or adverse events was observed after probiotics. There was insufficient evidence to assess the effects of probiotics on intestinal permeability. The overall quality of the evidence ranged from very low to low. Conclusions Probiotics may improve gastrointestinal symptoms in patients with celiac disease; however, our confidence in these results is limited by the low quality of the evidence. Further large clinical trials with a more rigorous design are needed to improve the quality of the evidence. Funding Agencies None
Exploring Performance Trade-offs in Tactical Edge Networks (2020)

Tactical edge networks are characterized by wireless links that have limited capacity and are prone to disconnection. In such a challenging and hostile environment, replication of information could be desirable as it increases information availability through redundancy and accessibility through proximity. However, replication of information has a negative effect on security because it broadens the attack surface - more nodes may be targeted to obtain sensitive information, thereby potentially increasing the overall risk of the information being compromised or leaked. Furthermore, replicating information takes away resources (particularly communications and power, but also to some extent computation and storage) from other tasks that might also need the same resources. These trade-offs between information availability, information protection, and resource utilization exist and need to be explored in the context of different solutions that could be applied to the challenging problem of information dispersal for assured operations in tactical environments.
Revenue Management's Renaissance (2008)

The era has ended when revenue management can stand alone as a tactical approach to room management. With technological and management support, revenue management must be and is being integrated into all aspects of hotel management marketing and operating strategies. Going beyond its role of managing room inventory, revenue management will consider total revenue contributions, including group business and its ancillary revenues. Because prices are essentially transparent, hotels will need to consider customer price elasticity and not simply match competitors' prices, with a goal of optimizing prices. Beyond that, revenue management can be used to manage all of the hotel's revenue streams, in part by considering the interaction of room sales and food and beverage sales. While revenue per available room (RevPAR) has been a good measure of performance, a revenue generation index, which compares competitors' RevPARs, is even more useful. Even more sophisticated is a revenue opportunity model, which monitors the effectiveness of inventory controls and analyzes the effects of revenue management decisions. Perhaps most promising is a customer-focused approach that tracks customers' purchases and targets promotions based on an understanding of customers' responses to prior offers.
Fig S4 from World Trade Center Dust Exposure Promotes Cancer in PTEN-deficient Mouse Prostates (2023)

&lt;p&gt;Fig. S4. Effect of direct introduction of WTC dust to the mouse prostate. A, Approach injecting solubilized WTC dust (2x 1 μl injections per prostate) and evaluation 6-8 weeks later. B, Histological low magnification image showing prostate enlargement after dust injection. C, Gross images showing a PBS control injected prostate (panel 1) and prostates with WTC dust injection (panels 2, 3, 4). D, Histological high magnification view showing immune cell infiltration in WTC dust injected prostate. E, Gene expression profiles for two independent prostates injected with WTC dust normalized to PBS control prostates (bars: B, C1, C3 = 2000 μM, C2, C4 = 5000 μM, D = 250 μM).&lt;/p&gt;
Neutrophil-to-lymphocyte ratio as a potential prognostic factor of disease-free survival in high-risk renal cell carcinoma: Analysis of the S-TRAC trial. (2018)

4562 Background: Sunitinib significantly improved disease-free survival (DFS) vs placebo (PBO) in patients (pts) with loco-regional renal cell carcinoma (RCC) at high risk of recurrence post nephrectomy. Neutrophil-to-lymphocyte ratio (NLR) is a marker of systemic inflammatory response. A post hoc exploratory analysis of the S-TRAC trial evaluated NLR as a potential prognostic factor in the RCC adjuvant setting. Methods: Sunitinib- and PBO-treated pts from S-TRAC were categorized into baseline (BL) NLR < 3 and ≥3 subgroups to explore the association between BL NLR (post nephrectomy) and DFS. Subgroups were based on low NLR ( < 3) being associated with long-term response in metastatic RCC. Associations between DFS and change in NLR from BL at Wk 4 were explored. Kaplan–Meier estimates were provided and Cox proportional analysis was performed. Results: In all, 605 pts from S-TRAC with BL NLR values were analyzed: 465 with NLR < 3 and 140 with NLR ≥3. At BL, significant differences between NLR < 3 vs ≥3 subgroups were seen for age (median 56.0 vs 60.0 y; P= .0161) and race (white [81.9% vs 90.0%], black [0.6% vs 0.7%], asian [14.6% vs 5.7%], other [2.8% vs 3.6%]; P= .0226). NLR < 3 vs ≥3 was statistically significant in the univariate analyses of DFS (hazard ratio [HR] 1.39; P= .0418); median 5.84 y (NLR < 3) vs not reached (NLR ≥3). A lower BL NLR was associated with shorter DFS. NLR < 3 vs ≥3 was also statistically significant in a multivariate analysis of DFS (HR 2.29; P= .0348). More pts treated with sunitinib (73%) had ≥25% decrease in NLR at Wk 4 vs PBO (20%). A ≥25% decrease in Wk 4 NLR showed a trend towards longer DFS vs no NLR change (HR 0.744; P= .0729), while a ≥25% increase in NLR at Wk 4 showed a trend towards shorter DFS vs no change (HR 1.112; P= .6771). NLR change from BL at Wk 4 was associated with treatment (sunitinib vs PBO; P< .0001). Conclusions: In S-TRAC, lower BL NLR might be a prognostic factor of shorter DFS. A ≥25% decrease in Wk 4 NLR showed a trend towards prolonged DFS. Additional data on CD8, neutrophils and lymphocytes will be presented. Clinical trial information: NCT00375674.
The C. elegans DAF-2 Insulin-Like Receptor is Abundantly Expressed in the Nervous System and Regulated by Nutritional Status (2011)

A Caenorhabditis elegans insulin-like signaling pathway regulates development, metabolism, and longevity. We detected abundant DAF-2 insulin-like receptor protein mainly in the nervous system, consistent with the assignment of DAF-2 pathway regulation of longevity to the nervous system. DAF-2 abundance in the nervous system is dependent on food intake, showing environmental modulation of pathway signaling. DAF-2 abundance is not dependent on downstream PI-3 kinase to DAF-16 transcription factor signaling. The modulation of DAF-2 protein level by nutritional status may constitute an important component in the irreversible commitment to dauer arrest.
Geant4 Analysis of n-Si Nuclear Reactions From Different Sources of Neutrons and Its Implication on Soft-Error Rate (2012)

This work examines nuclear events resulting from the interaction of atmospheric neutrons at ground level and different atmospheric-like sources with a silicon layer. Using extensive Geant4 simulations and in-depth data analysis, this study provides a detailed comparison between several facilities and natural environment in terms of nuclear processes, secondary ion production and fragment energy distribution. The different computed databases have been used in a second part of this work to estimate the Soft-Error Rate (SER) of a widely characterized 65 nm SRAM test circuit with the Tool suIte for rAdiation Reliability Assessment (TIARA Monte-Carlo simulation code). A detailed analysis is conducted to clarify the mechanisms leading to single and multiple cell upsets and to estimate the SER of a broad spectrum source from values obtained with monoenergetic simulations.
Security Enhanced Java: Mandatory Access Control for the Java Virtual Machine (2013)

Since 70's, and despite its operational complexity, Mandatory Access Control (MAC) has demonstrated its reliability to enforce integrity and confidentiality. Surprisingly, the Java technology, despite its popularity, has not yet adopted this protection principle. Current security features within the JVM (JAAS and bytecode verifier) can be bypassed, as demonstrated by summer 2012 attacks. Thus, a MAC model for Java and a cross platform reference monitor are required for the Java Virtual Machine. Security Enhanced Java (SEJava) enables to control dynamically the information flows between all the Java objects requiring neither bytecode nor source code instrumentations. The main idea is to consider Java types as security contexts, and method calls/field accesses as permissions. SEJava allows fine-grain MAC rules between the Java objects. Thus, SEJava controls all the information flows within the JVM. Our implementation is faster than concurrent approaches while allowing both finer and more advanced controls. A use case shows the efficiency to protect against Common Vulnerability and Exposures in an efficient manner.
Highly Selective Aldol Condensation Using Amine‐functionalized SiO<sub>2</sub>‐Al<sub>2</sub>O<sub>3</sub> Mixed‐oxide under Solvent‐free Condition (2010)

Abstract A series of amine catalysts supported on mesoporous molecular sieves SiO 2 /Al 2 O 3 with trimethoxysilylpropylamine [(CH 3 O) 3 Si(CH 2 ) 3 NH 2 ] loading varying from 3 mmol to 6 mmol were synthesized by impregnation method. The aldol condensation of various aromatic aldehydes and 1‐heptanal was used to test the acid‐base cooperativity of amine‐functionalized SiO 2 /Al 2 O 3 . The effects of solvent, reaction temperature, benzaldehyde to 1‐heptanal molar ratio, different supports (SiO 2 , Al 2 O 3 and SiO 2 ‐Al 2 O 3 ), catalyst amount and recyclability of the catalyst were investigated. Sample containing 5 mmol amine loaded showed highest benzaldehyde conversion (100%) and selectivity (97%) for jasminaldehyde.
Bacterial Vaginosis (2006)

Nguyen, Thaihang T. BS; Adelson, Martin E. PhD; Stemmer, Shlomo M. MD, MS; Mordechai, Eli PhD; Feola, Melanie BS Author Information