gebhart/patrepeval huggingface dataset:
Glucose/Xylose Co-Fermenting Saccharomyces cerevisiae Increases the Production of Acetyl-CoA Derived n-Butanol From Lignocellulosic Biomass (2022)

Efficient xylose catabolism in engineered <i>Saccharomyces cerevisiae</i> enables more economical lignocellulosic biorefinery with improved production yields per unit of biomass. Yet, the product profile of glucose/xylose co-fermenting <i>S. cerevisiae</i> is mainly limited to bioethanol and a few other chemicals. Here, we introduced an n-butanol-biosynthesis pathway into a glucose/xylose co-fermenting <i>S. cerevisiae</i> strain (XUSEA) to evaluate its potential on the production of acetyl-CoA derived products. Higher n-butanol production of glucose/xylose co-fermenting strain was explained by the transcriptomic landscape, which revealed strongly increased acetyl-CoA and NADPH pools when compared to a glucose fermenting wild-type strain. The acetate supplementation expected to support acetyl-CoA pool further increased n-butanol production, which was also validated during the fermentation of lignocellulosic hydrolysates containing acetate. Our findings imply the feasibility of lignocellulosic biorefinery for producing fuels and chemicals derived from a key intermediate of acetyl-CoA through glucose/xylose co-fermentation.
Approximate truncation robust computed tomography—ATRACT (2013)

We present an approximate truncation robust algorithm to compute tomographic images (ATRACT). This algorithm targets at reconstructing volumetric images from cone-beam projections in scenarios where these projections are highly truncated in each dimension. It thus facilitates reconstructions of small subvolumes of interest, without involving prior knowledge about the object. Our method is readily applicable to medical C-arm imaging, where it may contribute to new clinical workflows together with a considerable reduction of x-ray dose. We give a detailed derivation of ATRACT that starts from the conventional Feldkamp filtered-backprojection algorithm and that involves, as one component, a novel original formula for the inversion of the two-dimensional Radon transform. Discretization and numerical implementation are discussed and reconstruction results from both, simulated projections and first clinical data sets are presented.
Uteroplacental Adenovirus Vascular Endothelial Growth Factor Gene Therapy Increases Fetal Growth Velocity in Growth-Restricted Sheep Pregnancies (2014)

Fetal growth restriction (FGR) occurs in ∼8% of pregnancies and is a major cause of perinatal mortality and morbidity. There is no effective treatment. FGR is characterized by reduced uterine blood flow (UBF). In normal sheep pregnancies, local uterine artery (UtA) adenovirus (Ad)-mediated overexpression of vascular endothelial growth factor (VEGF) increases UBF. Herein we evaluated Ad.VEGF therapy in the overnourished adolescent ewe, an experimental paradigm in which reduced UBF from midgestation correlates with reduced lamb birthweight near term. Singleton pregnancies were established using embryo transfer in adolescent ewes subsequently offered a high intake (n=45) or control intake (n=12) of a complete diet to generate FGR or normal fetoplacental growth, respectively. High-intake ewes were randomized midgestation to receive bilateral UtA injections of 5×10¹¹ particles Ad.VEGF-A165 (n=18), control vector Ad.LacZ (n=14), or control saline (n=13). Fetal growth/well-being were evaluated using serial ultrasound. UBF was monitored using indwelling flowprobes until necropsy at 0.9 gestation. Vasorelaxation, neovascularization within the perivascular adventitia, and placental mRNA expression of angiogenic factors/receptors were examined using organ bath analysis, anti-vWF immunohistochemistry, and qRT-PCR, respectively. Ad.VEGF significantly increased ultrasonographic fetal growth velocity at 3-4 weeks postinjection (p=0.016-0.047). At 0.9 gestation fewer fetuses were markedly growth-restricted (birthweight >2SD below contemporaneous control-intake mean) after Ad.VEGF therapy. There was also evidence of mitigated fetal brain sparing (lower biparietal diameter-to-abdominal circumference and brain-to-liver weight ratios). No effects were observed on UBF or neovascularization; however, Ad.VEGF-transduced vessels demonstrated strikingly enhanced vasorelaxation. Placental efficiency (fetal-to-placental weight ratio) and FLT1/KDR mRNA expression were increased in the maternal but not fetal placental compartments, suggesting downstream effects on placental function. Ad.VEGF gene therapy improves fetal growth in a sheep model of FGR, although the precise mechanism of action remains unclear.
Lymphocyte Proliferation Responses Induced to Broadly Reactive Th Peptides Did Not Protect against Equine Infectious Anemia Virus Challenge (2005)

The effect of immunization with five lipopeptides, three containing T-helper (Th) epitopes and two with both Th and cytotoxic T-lymphocyte (CTL) epitopes, on equine infectious anemia virus (EIAV) challenge was evaluated. Peripheral blood mononuclear cells from EIAV lipopeptide-immunized horses had significant proliferative responses to Th peptides compared with those preimmunization, and the responses were attributed to significant responses to peptides Gag from positions 221 to 245 (Gag 221-245), Gag 250-269, and Pol 326-347; however, there were no consistent CTL responses. The significant proliferative responses in the EIAV lipopeptide-immunized horses allowed testing of the hypothesis that Th responses to immunization would enhance Th and CTL responses following EIAV challenge and lessen the viral load and the severity of clinical disease. The EIAV lipopeptide-immunized group did have a significant increase in proliferative responses to Th peptides 1 week after virus challenge, whereas the control group did not. Two weeks after challenge, a significant CTL response to virus-infected cell targets occurred in the EIAV lipopeptide-immunized group compared to that in the control group. These Th and CTL responses did not significantly alter either the number of viral RNA copies/ml or disease severity. Thus, lipopeptide-induced proliferative responses and enhanced Th and CTL responses early after virus challenge were unable to control challenge virus load and clinical disease.
The Polycistronic miRNA Cluster miR-17-92 Is Over-Expressed in Early Phase Chronic Myeloid Leukemia (CML) CD34+ Cells. (2006)

Abstract Micro RNAs (miRNAs) are small non-coding, single-stranded RNAs regulating gene expression by hybridization to complementary sequences in target mRNAs. Aberrant miRNA expression has been found in a variety of human malignancies including B-cell leukemias and lymphomas. The polycistronic miR-17–92 cluster, which includes seven miRNAs (miR-17-5p, miR-17-3p, miR-18a, miR-19a, miR-20a, miR-19b-1, miR-92-1), resides in intron 3 of the C13orf25 gene located on human chromosome 13 and has recently been described to harbor oncogenic potential in a murine transplantation model. In addition, expression of the polycistron can be regulated by c-myc, which is also activated by the Bcr-Abl oncogene product. To study miRNA expression in CML, K562 cells were analyzed by microarray analysis (miCHIP) for normalized expression of 244 miRNAs following treatment either with imatinib to inhibit Bcr-Abl kinase activity or with specific anti bcr-abl shRNA to knock-down gene expression. Both of these treatment strategies led to a 2–4-fold reduction of six mature miRNAs (miR-17-5p, miR-17-3p, miR-18a, miR-20a miR-19b-1, miR-92–1) as compared to untreated control cells. The reduction of the miR-17–92 miRNA cluster expression was confirmed for each individual mature miRNA species encoded in the cluster by real-time RT-PCR. Treatment with either imatinib or anti-bcr-abl shRNA also down-regulates expression of mature miRNA miR-19a (&amp;gt;3-fold) in K562 cells as quantified by real-time RT-PCR. We next used PCR based quantification to analyze miR-17–92 expression in purified normal (n=4) and CML CD34+ cells harvested at diagnosis of chronic phase disease (n=16). Individual mature miRNAs of the cluster were up-regulated (2–6-fold) in CML as compared to normal CD34+ cells. Additionally, the pri-miRNA for the miR-17–92 cluster was up-regulated in 70% (7/10) of CML samples. Interestingly, retrovirus-mediated over-expression of the miR-17-19b-1 cluster in K562 cells mediates enhanced colony-formation of transduced cells. Furthermore, K562 cells expressing high levels of the miR-17-19b-1 cluster are more resistant to proliferation inhibition induced by specific anti-myc RNAi, indicating some functional role of the miR-17-92 cluster on proliferation and survival in this model. In summary, the polycistronic miR-17–92 cluster is up-regulated in early chronic phase CML CD34+ cells and may contribute to cellular transformation by the Bcr-Abl oncogene product.
Quality of life in men with chronic scrotal pain (2017)

<b>Background</b>: Chronic scrotal pain (CSP) is a common and often debilitating condition found in up to 4.75% of men. There is little written on the impact of CSP on men's lives. <b>Aim</b>: The aim of this study was to understand the impact of CSP on men's lives. <b>Methods</b>: Patients with CSP were prospectively asked to complete a comprehensive questionnaire, including questions on quality of life (QoL), activities, and mood. <b>Results</b>: The mean age of the 131 patients was 43 years. Pain was intermittent, with severe pain episodes (mean pain scores 7.2 ± 2 out of 10) affecting men on average 40% ± 30% of the time. Overall, 88/131 (67.17%) of patients responded that they felt "unhappy" or "terrible" with their present situation. More than 40% of patients complained of depressive symptoms more than half the days of the month. Normal activities were adversely affected, with 68/131 (51.90%) reporting limited ability to work, 93/131 (70.99%) patients reporting decreased physical activity, and 81/131(61.83%) reporting decreased sexual activity. Comparing men with pain levels ≥ 7/10 vs. those with pain levels < 7/10, 47% (41/88) vs. 8.1% (3/37) reported that they felt "terrible," 40% (35/88) vs. 13% (5/38) had depressive feelings more than half the time, and 35% (28/80) vs. 16% (6/38) felt little pleasure doing things (<i>P</i> < 0.01 for all). <b>Conclusion</b>: Our study suggests that QoL, mood, and the ability to perform normal activities are profoundly disturbed in CSP patients and that the pain severity is directly related to QoL.
Characterization of the Human NEK7 Interactome Suggests Catalytic and Regulatory Properties Distinct from Those of NEK6 (2014)

Human NEK7 is a regulator of cell division and plays an important role in growth and survival of mammalian cells. Human NEK6 and NEK7 are closely related, consisting of a conserved C-terminal catalytic domain and a nonconserved and disordered N-terminal regulatory domain, crucial to mediate the interactions with their respective proteins. Here, in order to better understand NEK7 cellular functions, we characterize the NEK7 interactome by two screening approaches: one using a yeast two-hybrid system and the other based on immunoprecipitation followed by mass spectrometry analysis. These approaches led to the identification of 61 NEK7 interactors that contribute to a variety of biological processes, including cell division. Combining additional interaction and phosphorylation assays from yeast two-hybrid screens, we validated CC2D1A, TUBB2B, MNAT1, and NEK9 proteins as potential NEK7 interactors and substrates. Notably, endogenous RGS2, TUBB, MNAT1, NEK9, and PLEKHA8 localized with NEK7 at key sites throughout the cell cycle, especially during mitosis and cytokinesis. Furthermore, we obtained evidence that the closely related kinases NEK6 and NEK7 do not share common interactors, with the exception of NEK9, and display different modes of protein interaction, depending on their N- and C-terminal regions, in distinct fashions. In summary, our work shows for the first time a comprehensive NEK7 interactome that, combined with functional in vitro and in vivo assays, suggests that NEK7 is a multifunctional kinase acting in different cellular processes in concert with cell division signaling and independently of NEK6.
Structure and Assembly of Escherichia coli Capsules (2009)

The capsule is a cell surface structure composed of long-chain polysaccharides that envelops many isolates of Escherichia coli. It protects the cell against host defenses or physical environmental stresses, such as desiccation. The component capsular polysaccharides (CPSs) are major surface antigens in E. coli. They are named K antigens (after the German word Kapsel). Due to variations in CPS structures, more than 80 serologically unique K antigens exist in E. coli. Despite the hypervariability in CPS structures, only two capsule-assembly strategies exist in E. coli. These have led to the assignment of group 1 and group 2 capsules, and many of the key elements of the corresponding assembly pathways have been resolved. Structural features, as well as genetic and regulatory variations, give rise to additional groups 3 and 4. These employ the same biosynthesis processes described in groups 2 and 1, respectively. Each isolate possesses a distinctive set of cytosolic and inner-membrane enzymes, which generate a precise CPS structure, defining a given K serotype. Once synthesized, a multiprotein complex is needed to translocate the nascent CPS across the Gram-negative cell envelope to the outer surface of the outer membrane, where the capsule structure is assembled. While the translocation machineries for group 1 and group 2 CPSs are fundamentally different from one another, they possess no specificity for a given CPS structure. Each is conserved in all isolates producing capsules belonging to a particular group.
Exploring field correlation measurements on the electromagnetic ground state in non-local regime (2021)

In the terahertz range, electric field correlations on the electromagnetic ground state have been measured exploiting electrooptic sampling and femtosecond pulses. We investigate the dependence of these correlations on the probed space-time volume.
Multi-grid chain coding of binary shapes (2002)

This paper presents a chain code based approach to efficiently code binary shape information of video objects, in the context of object-based video coding. The proposed method tries to meet some of the requirements of the MPEG-4 standard, currently under development, notably efficient coding, and low delay. This approach allows several modes of operation depending on the application requirements, notably lossless, near-lossless, and lossy coding modes. For the lossless case a pure differential chain code method is proposed while for the near-lossless case a multi-grid chain code (MGCC) technique is adopted. Also both INTRA and INTER prediction modes can be used. For the INTER mode, motion compensation is applied without coding the residues. The MGCC is a near-lossless contour coding technique using a contour description based on edges, which combines both contour prediction and contour simplification.
ADAM AND AMS SCALE FOR ASSESSING ANDROPAUSE AMONG AGING INDIAN MEN (2015)

Objective : According to Indian Census 2011, India has 9% of population above the age of 60 years. Since andropause related effects are gradual and mimic many disease processes, clinical diagnosis is difficult to make. Very few studies have been done in North India to assess the awareness about andropause in males, which is why this study was conceived. To assess the awareness and knowledge about Andropause and its treatment modalities in males of Chandigarh. Methods : The present study was conducted at Urban Health Training Centre (UHTC-44 B) of Government Medical College and Hospital, Sector 32, Chandigarh (GMCH) in male patients attending outpatient department. This non-interventional, individual cross sectional study was done from Aug 2010- Aug 2011 in males 40 years and above. Systematic random sampling was done and study sample comprised of 757 males. The subjects were given pre-structured and pre-tested questionnaire that had questions pertaining to socio-demographic profile, Ageing Men Score scale (AMS scale), ADAM scale (Androgen Decline in Ageing Men), views about andropause and its treatment modalities. Results : Maximum subjects were from age group 40-49yrs (342; 45.17%), followed by those in age group of 60-69 years (141; 18.6%). 530 respondents (70%) indicated previous awareness regarding andropause or male menopause. Among andropause aware subjects, 440 (83.02%) respondents had poor knowledge about andropause and only 90 (16.98%) test takers actually had good knowledge about andropause. Age and marital status had little effect on knowledge of andropause. 627 (82.82%) had symptoms positive for andropause. Only 123 (19.61%) respondents were aware of treatment for andropause, 158 (25.21%) were willing to take treatment for andropause in form of testosterone injections or transdermal patches when informed about treatment options by health care workers. 360 (57.41%) respondents believed that healthy diet, exercise, herbal medications, Viagra and/or multivitamins can be used to treat andropause and refused to take testosterone injections. Remaining 239 (38.11%) respondents were not able to decide whether they want to take any treatment for andropause. Conclusion : Though awareness about andropause was seen among most men but the study shows the need for provision of health education to increase the knowledge of andropause among adult males.
Hepatic venous pressure gradient: clinical use in chronic liver disease (2014)

Portal hypertension is a severe consequence of chronic liver diseases and is responsible for the main clinical complications of liver cirrhosis. Hepatic venous pressure gradient (HVPG) measurement is the best available method to evaluate the presence and severity of portal hypertension. Clinically significant portal hypertension is defined as an increase in HVPG to >10 mmHg. In this condition, the complications of portal hypertension might begin to appear. HVPG measurement is increasingly used in the clinical fields, and the HVPG is a robust surrogate marker in many clinical applications such as diagnosis, risk stratification, identification of patients with hepatocellular carcinoma who are candidates for liver resection, monitoring of the efficacy of medical treatment, and assessment of progression of portal hypertension. Patients who had a reduction in HVPG of ≥ 20% or to ≤ 12 mmHg in response to drug therapy are defined as responders. Responders have a markedly decreased risk of bleeding/rebleeding, ascites, and spontaneous bacterial peritonitis, which results in improved survival. This review provides clinical use of HVPG measurement in the field of liver disease.
Synchronization Implications of Providing Circuit Emulation Services in an IP network (2005)

There is general agreement that a Next Generation Network (NGN) will have, at its core, a packet-switched architecture. This agreement was underscored at the ITU-T Workshop on Next Generation Networks held in July 2003, [1]. There is general agreement, also emphasized in this Workshop, that legacy services shall be supported for many years to come and, further, that the evolution of the Network to its “converged” form shall provide quality of service capabilities that would make the NGN transparent to these legacy services. These legacy services include, but are not limited to, constant-bit-rate (CBR) services whereby legacy end-user equipment such as E1/T1 multiplexers and integrated access devices, Private Branch Exchange (PBX) equipment, and ISDN terminals, continue to exist and demand service at a quality level provided in today’s (circuit-switched) Public Switched Telephone Network (PSTN).
Pinocchio's Pupil: Using Eyetracking and Pupil Dilation To Understand Truth-telling and Deception in Games (2006)

We conduct laboratory experiments on sender-receiver games with an incentive for senders to exaggerate (such as security analysts painting a rosy picture about earnings prospects). Our results show that “overcommunication”—messages are more informative of the true state than they should be, in equilibrium—is consistent with a level-k model. Eyetracking shows that senders look much more on the payoff rows corresponding to the true state, and much less at receiver payoffs than at their own payoffs. Senders ’ pupils also dilate more when their deception is larger in magnitude. Together, these data are consistent with the hypothesis that figuring out how to deceive another player is cognitively difficult as assumed in the level-k model. A combination of sender messages and lookup patterns predicts the true state about twice as often as predicted by equilibrium. Using these measures would enable receiver subjects to hypothetically earn
Sexual dimorphism of the cuticle and body-wall muscle in free-living mycophagous nematodes (2019)

Sexual dimorphism in motility-related traits is widespread among animals, including several species of Nematoda. However, no study has examined motility-related structural components and compared them between sexes. We examined the motility-related components in four species: Bursaphelenchus conicaudatus Kanzaki, Tsuda and Futai, 2000; Bursaphelenchus rainulfi Braasch and Burgermeister, 2002; Bursaphelenchus doui Braasch, Gu, Burgermeister and Zhang, 2005; Parasitaphelenchus costati Kanzaki, Ekino, Ide, Masuya and Degawa, 2018. We measured the structure and amount of cuticle and body-wall muscles and estimated their relationship to body diameter or total cross-sectional area. Although no structural differences were observed in muscle, the relevant muscle area of B. doui and P. costati was significantly smaller in females than in males. This difference was greatest in P. costati. In all but B. doui, the relative cuticle thickness was significantly smaller in females than in males. Furthermore, only P. costati females had no striated basal zones in their cuticles; these are thought to be cross-linked proteins that provide strength to nematode cuticle during body movement. These results indicate that sexual dimorphism in motility-related structural components is present in P. costati and that females invest less energy in the components than do males.
Development of chitosan-alginate based biosorbent for the removal of p-chlorophenol from aqueous medium (2009)

Removal of p-chlorophenol (pCP) from synthetic aqueous solutions was studied through adsorption on a biosorbent developed from chitosan (CS) and sodium alginate (SA), the natural cationic and anionic polysaccharides, respectively. Chitosan-coated sodium alginate beads were prepared and treated with calcium chloride solution in order to improve the stability as well as hydrophobic character. The resulting beads (CS/CA) were characterized using FTIR spectra, scanning electron microscopy (SEM), and BET surface analysis. The efficiency of this biosorbent in removing pCP from aqueous medium was studied under batch equilibrium and dynamic column flow experimental conditions. The binding capacity of the biosorbent was studied as a function of initial pH, contact time, initial concentration of adsorbate and amount of biomass. The data were fitted to pseudo-first-order, pseudo-second-order, and Weber–Morris models and found that the adsorption process followed pseudo-first-order kinetics. Further, the equilibrium data were fitted to Freundlich, Langmiur, and Dubinin–Radushkevich (D–R) adsorption isotherms and the isotherm constants were evaluated for adsorption of pCP. The maximum monolayer adsorption capacity of CS/CA beads was found to be 127 mg g−1. Column flow results were used to generate breakthrough curves. The experimental results suggested that the chitosan–calcium alginate blended biosorbent was effective for the removal of pCP from aqueous medium.