gebhart/patrepeval huggingface dataset:
Trial by phylogenetics - Evaluating the Multi-Species Coalescent for phylogenetic inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae) (2019)

ABSTRACT From publicly available next-gen sequencing datasets of non-model organisms, such as marine protists, arise opportunities to explore their evolutionary relationships. In this study we explored the effects that dataset and model selection have on the phylogenetic inference of the Gonyaulacales, single celled marine algae of the phylum Dinoflagellata with genomes that show extensive paralogy. We developed a method for identifying and extracting single copy genes from RNA-seq libraries and compared phylogenies inferred from these single copy genes with those inferred from commonly used genetic markers and phylogenetic methods. Comparison of two datasets and three different phylogenetic models showed that exclusive use of ribosomal DNA sequences, maximum likelihood and gene concatenation showed very different results to that obtained with the multi-species coalescent. The multi-species coalescent has recently been recognized as being robust to the inclusion of paralogs, including hidden paralogs present in single copy gene sets (pseudoorthologs). Comparisons of model fit strongly favored the multi-species coalescent for these data, over a concatenated alignment (single tree) model. Our findings suggest that the multi-species coalescent (inferred either via Maximum Likelihood or Bayesian Inference) should be considered for future phylogenetic studies of organisms where accurate selection of orthologs is difficult.
Abstract 17184: Nearly One Third of GWAS CAD Are Putative SMC Klf4 or Oct4 Targets in Advanced Atherosclerotic Lesions (2018)

Atherosclerosis is a disease of chronic inflammation and the leading cause of morbidity and mortality worldwide. Despite decades of research, our understanding of the mechanisms regulating plaque stability remains poor. Until recently, smooth muscle cells (SMCs) were thought to play an athero-protective role in lesion pathogenesis. However, rigorous lineage tracing has shown a significant portion (&amp;gt;80%) of SMC-derived cells within an advanced atherosclerotic lesion did not express detectable SMC markers. Furthermore, SMC-specific conditional KO of Klf4 resulted in reduction of several indices of plaque instability and SMC-derived macrophage-like cells. In contrast, conditional KO of Oct4 in SMCs presented a reduction of SMC and increased of Lgals3+ cells within lesions, as well as increase of several indices of plaque instability. Taken together, SMCs can have a beneficial or detrimental effect in lesion pathogenesis. Hypothesis: Combinatorial analysis of Oct4/Klf4 ChIP-seq and RNA-seq of advanced atherosclerotic lesions from our SMC-Klf4 and SMC-Oct4 mice provide a unique opportunity to identify genes that play a critical role in regulating beneficial or detrimental changes in SMC phenotype. Results: SMC-Oct4 target genes are enriched for migration pathways, while SMC-Klf4 target genes are enriched for inflammation pathways. Further, atherosclerosis pathway, among others, presented significant opposite patterns (SMC-Oct4-KO up-regulation and SMC-Klf4-KO down-regulation), and presented strong significant gene anti-correlation, corroborating our phenotypic observations. Remarkably, we cross-reference our ChIP-seq datasets with CAD GWAS and found that 54 of the 161 human loci were either Klf4 and/or Oct4 SMC targets, highly suggesting that CAD GWAS genes might be affecting SMC function in lesion development/pathogenesis. To validate our results, we used the STARNET dataset, and we observed that both Oct4 and Klf4 are significantly up-regulated in aorta of CAD patients compared to controls. In addition, co-expression analysis shows that one of the Klf4 network is highly related to human GWAS CAD, including genes such as LDLR, APOE, PCSK9, TRIB1, and others. Surprisingly, more than 35% of genes in this network also are present in our SMC Klf4 ChIP-seq dataset. Conclusions: our results suggests that: late stage atherosclerotic lesions of mouse and humans seems to be more similar than previously thought; and nearly 1/3 of CAD GWAS loci appear to be affecting SMC function and are potentially Klf4/Oct4-dependent.
An Approach for Homology Search with Reconfigurable Hardware (2001)

Smith Waterman Algorithm[1] is an efficient and useful algorithm for homology search problems. However, it can not be processed within reasonable time on desktop computer systems, therefore, dedicated hardware systems which is very expensive are used in general. In this paper, we propose a homology search system with reconfigurable hardware. For reducing the cost, the system is composed of off-the-shelf components. As the result, we could reduce the cost to thousands of dollars and achieved 330 times speedup compared with a desktop computer with a 1GHz PentiumIII. The performance is almost comparable with small to middle class dedicated hardware systems.
Locating subverted processes using random packet comparison in SCADA systems (2013)

A supervisory control and data acquisition (SCADA) system may be subject to integrity attacks. Anomalies in sensor measurements may be used to detect these attacks, but such techniques do not permit us to locate attacking nodes. We propose a novel technique to enable this. Each participating network node probabilistically copies packets and marks them with routing information, before encrypting them with private keys and forwarding them to the operator. Nodes regularly release the keys used to encrypt packets. At that point, the operator may compare the copied packets with the original. Using the differences in packet content and routing information, it is possible to deduce to within one or two processes the location of an attack. Our approach is based on IP traceback techniques originally used for detecting the origin of denial of service attacks. The complexity of the approach is low and the technique can be shown to be resilient to counter-attack.
prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacter sphaeroides (1994)

A new locus, prrA, involved in the regulation of photosynthesis gene expression in response to oxygen, has been identified in Rhodobacter sphaeroides. Inactivation of prrA results in the absence of photosynthetic spectral complexes. The prrA gene product has strong homology to response regulators associated with signal transduction in other prokaryotes. When prrA is present in multiple copies, cells produce light-harvesting complexes under aerobic growth conditions, suggesting that prrA affects photosynthesis gene expression positively in response to oxygen deprivation. Analysis of the expression of puc::lacZ fusions in wild-type and PrrA- cells revealed a substantial decrease in LacZ expression in the absence of prrA under all conditions of growth, especially when cells were grown anaerobically in the dark in the presence of dimethyl sulfoxide. Northern (RNA) and slot blot hybridizations confirmed the beta-galactoside results for puc and revealed additional positive regulation of puf, puhA, and cycA by PrrA. The effect of truncated PrrA on photosynthesis gene expression in the presence of low oxygen levels can be explained by assuming that PrrA may be effective as a multimer. PrrA was found to act on the downstream regulatory sequences (J. K. Lee and S. Kaplan, J. Bacteriol. 174:1146-1157, 1992) of the puc operon regulatory region. Finally, two spontaneous prrA mutations that abolish prrA function by changing amino acids in the amino-terminal domain of the protein were isolated.
2,4-Diazapentadienes. I. Prototropy, Cyclization, and Addition–Elimination (1972)

The preparations and reactions of a series of 1,3,5-triaryl-2,4-diaza-1,3-pentadienes (1) have been investigated. Products of cyclization (2 and 4), prototropy 3 and addition–elimination (5, 6, and 7) have been characterized. Also, the preparations and reactions of 3, a new isomer of 1, have been studied.
Peroxisome Proliferator-Activated Receptor-γ Ligands Reduce Neuronal Inducible Nitric Oxide Synthase Expression and Cell DeathIn Vivo (2000)

Expression of the inducible form of nitric oxide synthase (iNOS) in brain may contribute to neurotoxicity in Alzheimer9s disease (AD). Expression of iNOS can be induced in cerebellar granule cells (CGCs)<i>in vivo</i> as well as <i>in vitro</i>, allowing these cells to be used to study regulation of neuronal iNOS expression. We report here that microinjection of bacterial lipopolysaccharide and interferon gamma into rat cerebellum induced iNOS expression in CGCs and subsequent cell death assessed by staining for DNA fragmentation. Co-injection of three structurally distinct agonists of the peroxisome proliferator-activated receptor gamma (PPARγ), including the antidiabetic thiazolidinedione troglitazone, the nonsteroidal anti-inflammatory drug (NSAID) ibuprofen, and the prostanoid 15-deoxy-Δ<sup>12,14</sup> prostaglandin J<sub>2</sub>, reduced both iNOS expression and cell death<i>,</i> whereas co-injection of the selective cyclo-oxygenase inhibitor NS-398 had no effect. These data demonstrate that PPARγ agonists can modulate inflammatory responses in brain. Because sustained medication with NSAIDs reduces the risk and delays the onset of AD, these results further suggest that NSAIDs provide therapeutic value by binding to PPARγ present in AD brain, thereby preventing iNOS expression and neuronal cell death.
Exploring the Past, Present, and Future of Anti-Angiogenic Therapy in Glioblastoma (2023)

Glioblastoma, a WHO grade IV astrocytoma, constitutes approximately half of malignant tumors of the central nervous system. Despite technological advancements and aggressive multimodal treatment, prognosis remains dismal. The highly vascularized nature of glioblastoma enables the tumor cells to grow and invade the surrounding tissue, and vascular endothelial growth factor-A (VEGF-A) is a critical mediator of this process. Therefore, over the past decade, angiogenesis, and more specifically, the VEGF signaling pathway, has emerged as a therapeutic target for glioblastoma therapy. This led to the FDA approval of bevacizumab, a monoclonal antibody designed against VEGF-A, for treatment of recurrent glioblastoma. Despite the promising preclinical data and its theoretical effectiveness, bevacizumab has failed to improve patients' overall survival. Furthermore, several other anti-angiogenic agents that target the VEGF signaling pathway have also not demonstrated survival improvement. This suggests the presence of other compensatory angiogenic signaling pathways that surpass the anti-angiogenic effects of these agents and facilitate vascularization despite ongoing VEGF signaling inhibition. Herein, we review the current state of anti-angiogenic agents, discuss potential mechanisms of anti-angiogenic resistance, and suggest potential avenues to increase the efficacy of this therapeutic approach.
Neuroserpin (PI‐12) is upregulated in high‐grade prostate cancer and is associated with survival (2005)

We carried out Genechip analysis using prostate cancer and non-malignant tissue to identify specific genes related to prostate cancer. We focused on neuroserpin (PI-12), which has been identified as one of the genes with high expression in prostate cancer. We analyzed the relationship between its expression pattern and clinical characteristics. Prostate cancer and normal prostate tissue were analyzed by Affymetrix GeneChip technology. We carried out real-time quantitative PCR on a total of 102 specimens: 45 of normal prostate, 45 of previously untreated prostate cancer (constituting 45 pairs of samples obtained at radical prostatectomy, with each pair dissected from the same prostate specimen) and 12 of recurrent hormone refractory prostate cancer (HRPC). Results showed that the neuroserpin gene was more highly expressed in prostate cancer than in normal prostate tissue. Neuroserpin expression in untreated prostate cancer was significantly higher than that in normal prostate. In HRPC it was significantly higher than that in untreated prostate cancer and normal prostate. In untreated prostate cancer, neuroserpin expression was significantly higher in high grade tumors such as poorly differentiated adenocarcinoma than in lower grade tumors such as well or moderately differentiated adenocarcinoma. Higher neuroserpin expression was associated with shorter recurrence-free survival after radical prostatectomy, shorter recurrence-free survival in HRPC patients and shorter overall survival in HRPC patients. The neuroserpin gene may be associated with the development, progression and aggressiveness of prostate cancer. Our present data suggests that higher neuroserpin expression may predict an unfavorable outcome after radical prostatectomy or hormone therapy.
High Throughput Preparation of Poly(Lactic-Co-Glycolic Acid) Nanoparticles Using Fiber Fluidic Reactor (2020)

Polymeric nanoparticles (NPs) have a variety of biomedical, biotechnology, agricultural and environmental applications. As such, a great need has risen for the fabrication of these NPs in large scales. In this study, we used a high throughput fiber reactor for the preparation of poly(lactic-<i>co</i>-glycolic acid) (PLGA) NPs via nanoprecipitation. The fiber reactor provided a high surface area for the controlled interaction of an organic phase containing the PLGA solution with an aqueous phase, containing poly(vinyl alcohol) (PVA) as a stabilizer. This interaction led to the self-assembly of the polymer into the form of NPs. We studied operational parameters to identify the factors that have the greatest influence on the properties of the resulting PLGA NPs. We found that the concentration of the PLGA solution is the factor that has the greatest effect on NP size, polydispersity index (PDI), and production rate. Increasing PLGA concentration increased NP sizes significantly, while at the same time decreasing the PDI value. The second factor that was found to affect NP properties was the concentration of PVA solution, which resulted in increased NP sizes and decreased production rates. Flowrates of the feed streams also affected NP size to a lesser extent, while changing the operational temperature did not change the product's features. In general, the results demonstrate that fiber reactors are a suitable method for the large-scale, continuous preparation of polymeric NPs suitable for biomedical applications.
Evaluation of spatial brucellosis distribution using the Geographic Information System: Towards building a high performance spatial epidemiology system for supervision on zoonotic infections (2014)

Brucellosis, a bacterial zoonosis, remains a public health threat worldwide, particularly in Kazakhstan and Central Asia. The disease can manifest in a variety of forms, from asymptomatic to severe organic forms. The republic is still included into ten countries with the highest incidence levels for the first time diagnosed human brucellosis, which emphasizes the magnitude of the problem. This study was conducted using Geographic Information System (GIS) techniques, in order to evaluate the spatial distribution of the disease in the rural area of Almaty and Zhambyl oblasts (provinces). The spatial distribution of Brucella melitensis biovars was studied for 2011-2013 (continuous sampling), as well as the incidence rate of the first time diagnosed human brucellosis and the prevalence of this infection in livestock, per long-time annual average values. For the data visualization we use free software, QuantumGIS of versions 1.8.0 (Lisboa) and 2.0.1 (Dufour). A GIS-based spatial analysis was carried out to identify geographic distribution patterns of brucellosis infection in humans and animals. Local Moran's I statistic was employed using GeoDa software to evaluate cluster analysis. Incidence rates were empirically Bayes smoothed for human, cattle, and a combined sheep/goat group. Results of the spatial autocorrelation analysis for 2007-2013 showed high incidence rates for humans and animals were geographically clustered in the southwest region, where human clusters decreased in later years. While this may reflect an improving human disease situation or only annual reporting differences, these results suggest that human and animal incidence is closely associated. The use of spatial autocorrelation proved a great benefit for better visualization of the endemic, especially in elucidating the actual distribution of brucellosis cases in the rayons (districts) and providing an effective tool for planning the monitoring of the disease at a local level.
A Simplified line-to-line space vector modulation for multilevel converter applied for a standalone wind energy conversion system (2019)

A new Simplified Direct Space Vector Modulation (SDSVM), based on a line-to-line space-vector diagram, is proposed, in this paper, to control a three-level Neutral-Point-Clamped (NPC) Converter for a standalone variable speed Wind Energy Conversion System (WECS). The frequency and magnitude of the stator output voltage of the Doubly Fed Induction Generator (DFIG) are controlled and fixed at nominal values, despite the variable rotor speed, ensuring by that a continuous AC supply for three phase loads. The performance of the proposed SDSVM technique to control the standalone DFIG based WECS is demonstrated through simulation results. The control strategy is implemented on a dSPACE DS 1104 board driving a 4.5 kW DFIG based wind system test bench. The obtained experimental results confirm the validity of the control.
3 Months of Nitrate plus Exercise Training Improves Hemodynamic Profile in Peripheral Arterial Disease (2016)

Peripheral artery disease (PAD) is a form of cardiovascular disease caused by atherosclerotic occlusions that impair blood flow to the lower extremities. It is characterized by endothelial dysfunction and an inability to endogenously produce nitric oxide (NO). NO bioavailability is essential for vascular health and can be increased exogenously via oral nitrate supplementation and its subsequent conversion to plasma nitrite and NO. We have previously shown changes in resting hemodynamics following chronic exercise training and after an acute oral nitrate beverage. PURPOSE: To determine the effects of 3 months of supervised exercise training plus chronic dietary provision of an inorganic nitrate (4.2mmol in the form of concentrated beetroot juice, BR) beverage (EX+BR) versus exercise training and placebo beverage (EX+PL) on resting hemodynamics and hyperemic blood flow in subjects with PAD. The study was a double-blind, randomized controlled trial (data is a subset of a larger clinical trial). METHODS: At baseline testing, all subjects underwent measures of resting ankle-brachial index (ABI), aortic blood pressures (ASBP) and calf muscle blood flow during reactive hyperemia following 5 minutes of ischemia (RHBF). Subjects were then randomized to either the EX+BR (n=11) or EX+PL (n=12) group. Exercise training involved 3 sessions per week consisting of at least 30 minutes walking at a moderate claudication pain level. Subjects consumed BR or PL 3 hours prior to each exercise session. The 3-month testing protocol was identical to baseline. Comparisons were made using a two-way ANOVA with repeated measures. RESULTS: There were no differences in baseline measures for ABI, ASBP or RHBF between groups. At 3M, ABI increased 0.10±0.15 (p=0.05) and 0.15±0.11 (p≤0.01), RHBF 0.74±2.80% (ns) and 2.44±2.77% (p≤0.05) for the EX+PL and EX+BR respectively (ES = -0.69, CI = -0.17 to +1.51). Resting ASBP were significantly lower at 3M for EX±BR versus EX+PL (128.45±17.31 v 147.67±23.27mmHg, p0.05, ES = -0.95, CI = -1.76 to -0.04). CONCLUSION: Chronic administration of a high nitrate drink plus supervised exercise training improved the hemodynamic profile in subjects with PAD more than exercise training alone.Supported by grants R21HL111972 and R21HL113717 to JDA
Stimulated scattering in magnetoactive semiconductors (1993)

An analytical investigation of the stimulated Raman (SRS) and Brillouin (SBS) scatterings of the Stokes mode is undertaken in centrosymmetric semiconductors with a dc magnetic field applied along the direction of the uniform pump field. The threshold field for inciting SRS and SBS and the corresponding gain constants have also been identified. The magnetic field is found to reduce the threshold field and subsequently augment the gain constant of the scattered mode. The magnitude of the third-order nonlinear optical susceptibility determined from our analysis is found to agree with the theoretically and experimentally quoted values. The growth rates of the Raman and the Brillouin modes are found to be higher in the heavily doped regime. The SBS gain constant is found to be higher than SRS and its ratio is found to be equal to the ratio of the optical to acoustical wave frequency. The SBS and SRS gain constants are found to be effectively influenced by operating the magnetic field such that the cyclotron frequency becomes comparable to the acoustical (for SBS) or optical (for SRS) wave frequency.
Starch Synthesis in Developing Potato Tubers (1979)

Abstract The activities of enzymes involved in starch metabolism were measured at intervals during tuberization and the early stages of tuber growth in Solanum tubersum grown in water culture under controlled environmental conditions. Starch synthase, ADPglucose pyrophosphorylase, UDPglucose pyrophosphorylase and phosphorylase activities all increased during tuber development, the most pronounced increases occurring in the activities of ADP‐glucose pyrophosphorylase and phosphorylase. The activity ratio ADPglucose pyrophosphorylase/phosphorylase was lowest in slow growing tubers and hightest in fast growing tubers. In addition, high sugar concentrations in fast growing tubers and low sugar concentrations in slow growing tubers suggested that enzyme levels might be influenced by sugar concentration. The activities of starch synthase, phosphorylase and ADPglucose pyrophosphorylase were increased 2–2.5 fold by the presence of 100 m M K + . It is concluded that the major enzyme changes occur as a consequence of tuber initiation and that starch accumulation is controlled, at least in part, by the activities of ADPglucose pyrophosphorylase and phosphorylase.
Mid-infrared supercontinuum generation in tapered chalcogenide fiber for producing octave-spanning frequency comb around 3 μm (2012)

We demonstrate mid-infrared (mid-IR) supercontinuum generation (SCG) with instantaneous bandwidth from 2.2 to 5 μm at 40 dB below the peak, covering the wavelength range desirable for molecular spectroscopy and numerous other applications. The SCG occurs in a tapered As(2)S(3) fiber prepared by in-situ tapering and is pumped by femtosecond pulses from the subharmonic of a mode-locked Er-doped fiber laser. Interference with a narrow linewidth c.w. laser verifies that the coherence properties of the near-IR frequency comb have been preserved through these cascaded nonlinear processes. With this approach stable broad mid-IR frequency combs can be derived from commercially available near-IR frequency combs without an extra stabilization mechanism.