gebhart/patrepeval huggingface dataset:
Gene expression over the course of schizophrenia: from clinical high-risk for psychosis to chronic stages (2019)

The study of patients with schizophrenia (SZ) at different clinical stages may help clarify what effects could be due to the disease itself, to the pharmacological treatment, or to the disease progression. We compared expression levels of targeted genes in blood from individuals in different stages of SZ: clinical high risk for psychosis (CHR), first episode of psychosis (FEP), and chronic SZ (CSZ). Then, we further verified whether single-nucleotide polymorphisms (SNPs) could be related to gene expression differences. We investigated 12 genes in 394 individuals (27 individuals with CHR, 70 antipsychotic-naive individuals with FEP, 157 CSZ patients, and 140 healthy controls (HCs)). For a subsample, genotype data were also available, and we extracted SNPs that were previously associated with the expression of selected genes in whole blood or brain tissue. We generated a mediation model in which a putative cause (SNP) is related to a presumed effect (disorder) via an intermediate variable (gene expression). MBP and NDEL1 were upregulated in FEP compared to all other groups; DGCR8 was downregulated in FEP compared to HC and CHR; DGCR2 was downregulated in CSZ compared to FEP and HCs; DISC1 was upregulated in schizophrenia compared to controls or FEP, possibly induced by the rs3738398 and rs10864693 genotypes, which were associated with DISC1 expression; and UFD1 was upregulated in CSZ and CHR compared to FEP and HC. Our results indicated changes in gene expression profiles throughout the different clinical stages of SZ, reinforcing the need for staging approaches to better capture SZ heterogeneity.
Prevalence of HPV 16 and 18 and attitudes toward HPV vaccination trials in patients with cervical cancer in Mali (2017)

This study provides strong support for the introduction of currently available HPV vaccines in Mali, and also provides key information about conditions for obtaining informed consent for HPV vaccine trials and HPV vaccination in Mali.
A Novel Technique for Redox Lipidomics Using Mass Spectrometry: Application on Vegetable Oils Used to Fry Potatoes (2021)

Vegetables oils, rich in polyunsaturated fatty acids, are vulnerable to oxidation during manufacturing, processing, and food preparation. Currently, individual oxidation products are not well characterized, and hence, the health impacts of these unique lipid species remain unknown. Here, we introduce an extensive oxidized lipidomics <i>in silico</i> tandem mass spectrometry library and integrate these libraries within a user-friendly software covering a comprehensive redox lipidomics workflow. We apply this workflow to olive, soy, and walnut cooking oil; comparing unheated oil, oil after deep frying potatoes, and oil after oven frying potatoes. We annotated over a thousand oxidized triglycerides across 273 features (many coeluted). This software was validated against traditional chemical assays of oxidation, known oxidized lipids in castor oil, synthesized standards, and an alternate software LPPtiger. Development of these new software programs for redox lipidomics opens the door to characterize health implications of individual oxidation products.
Toward whole‐cortex enhancement with an ultrahigh dielectric constant helmet at 3T (2019)

A prototype uHDC helmet enhanced the SNR of a standard head coil to the level of a high density 64-channel coil, although transmit homogeneity was compromised. Further improvements in SNR may be achievable with optimization of this technology, and could be a low-cost approach for future radiofrequency engineering work in the brain at 3T.
The capability of detecting small vessels beyond the conventional MRI sensitivity using iron‐based contrast agent enhanced susceptibility weighted imaging (2020)

Imaging brain microvasculature is important in cerebrovascular diseases. However, there is still a lack of non-invasive, non-radiation, and whole-body imaging techniques to investigate them. The aim of this study is to develop an ultra-small superparamagnetic iron oxide (USPIO) enhanced susceptibility weighted imaging (SWI) method for imaging micro-vasculature in both animal (~10 μm in rat) and human brain. We hypothesized that the USPIO-SWI technique could improve the detection sensitivity of the diameter of small subpixel vessels 10-fold compared with conventional MRI methods. Computer simulations were first performed with a double-cylinder digital model to investigate the theoretical basis for this hypothesis. The theoretical results were verified using in vitro phantom studies and in vivo rat MRI studies (n = 6) with corresponding ex vivo histological examinations. Additionally, in vivo human studies (n = 3) were carried out to demonstrate the translational power of the USPIO-SWI method. By directly comparing the small vessel diameters of an in vivo rat using USPIO-SWI with the small vessel diameters of the corresponding histological slide using laser scanning confocal microscopy, 13.3-fold and 19.9-fold increases in SWI apparent diameter were obtained with 5.6 mg Fe/kg and 16.8 mg Fe/kg ferumoxytol, respectively. The USPIO-SWI method exhibited its excellent ability to detect small vessels down to about 10 μm diameter in rat brain. The in vivo human study unveiled hidden arterioles and venules and demonstrated its potential in clinical practice. Theoretical modeling simulations and in vitro phantom studies also confirmed a more than 10-fold increase in the USPIO-SWI apparent diameter compared with the actual small vessel diameter size. It is feasible to use SWI blooming effects induced by USPIO to detect small vessels (down to 10 μm in diameter for rat brain), well beyond the spatial resolution limit of conventional MRI methods. The USPIO-SWI method demonstrates higher potential in cerebrovascular disease investigations.
Evaluation of the potential therapeutic role of a new generation of vitamin D analog, MART-10, in human pancreatic cancer cells in vitro and in vivo (2013)

Pancreatic cancer is a lethal disease with no known effective chemotherapy and radiotherapy, and most patients are diagnosed in the late stage, making them unsuitable for surgery. Therefore, new therapeutic strategies are urgently needed. 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3] is known to possess antitumor actions in many cancer cells in vitro and in vivo models. However, its clinical use is hampered by hypercalcemia. In this study, we investigated the effectiveness and safety of a new generation, less calcemic analog of 1α,25(OH)2D3, 19-nor-2α-(3-hydroxypropyl)-1α,25-dihydroxyvitamin D3 (MART-10), in BxPC-3 human pancreatic carcinoma cells in vitro and in vivo. We demonstrate that MART-10 is at least 100-fold more potent than 1α,25(OH)2D3 in inhibiting BxPC-3 cell proliferation in a time- and dose-dependent manner, accompanied by a greater upregulation of cyclin-dependent kinase inhibitors p21 and p27 and a greater downregulation of cyclin D3 and cyclin-dependent kinases 4 and 5, leading to a greater increase in the fraction of cells in G0/G1 phase. No induction of apoptosis and no effect on Cdc25 phosphatases A and C were observed in the presence of either MART-10 or 1α,25(OH)2D3. In a xenograft mouse model, treatment with 0.3 µg/kg body weight of MART-10 twice/week for 3 weeks caused a greater suppression of BxPC-3 tumor growth than the same dose of 1α,25(OH)2D3 without inducing hypercalcemia and weight loss. In conclusion, MART-10 is a promising agent against pancreatic cancer growth. Further clinical trial is warranted.
The covalent modification and regulation of TLR8 in HEK-293 cells stimulated with imidazoquinoline agonists (2007)

The mammalian TLRs (Toll-like receptors) mediate the rapid initial immune response to pathogens through recognition of pathogen-associated molecular patterns. The pathogen pattern to which TLR8 responds is ssRNA (single-stranded RNA) commonly associated with ssRNA viruses. TLR8 also responds to small, purine-like molecules including the imidazoquinoline IRMs (immune-response modifiers). The IRMs include molecules that selectively activate TLR7, selectively activate TLR8 or non-selectively activate both TLR7 and TLR8. Using HEK-293 cells (human embryonic kidney cells) stably expressing an NF-kappaB (nuclear factor kappaB)/luciferase promoter-reporter system as a model system, we have examined the regulation of TLR8 using the non-selective TLR7/8 agonist, 3M-003. Using conservative tyrosine to phenylalanine site-directed mutation, we show that of the 13 tyrosine residues resident in the cytosolic domain of TLR8, only three appear to be critical to TLR8 signalling. Two of these, Tyr898 and Tyr904, reside in the Box 1 motif and the third, Tyr1048, lies in a YXXM putative p85-binding motif. TLR8 is tyrosine-phosphorylated following 3M-003 treatment and TLR8 signalling is inhibited by tyrosine kinase inhibitors. Treatment with 3M-003 results in the association of the p85 regulatory subunit of PI3K (phosphoinositide 3-kinase) with TLR8 and this association is inhibited by tyrosine to phenylalanine mutation of either the YXXM or Box 1 motifs. As a further consequence of activation by 3M-003, TLR8 is modified to yield both higher and lower molecular mass species. These species include a monoubiquitinated form as deduced from ubiquitin peptide sequencing by HPLC/MS/MS (tandem MS).
Nonlinear pulse shaping and polarization dynamics in mode-locked fibre lasers (2013)

We review our recent progress on the study of new nonlinear mechanisms of pulse shaping in passively mode-locked fibre lasers. These include a mode-locking regime featuring pulses with a triangular distribution of the intensity, and spectral compression arising from nonlinear pulse propagation. We also report on our recent experimental studies unveiling new families of vector solitons with precessing states of polarization for multi-pulsing and bound-state soliton operations in a carbon nanotube mode-locked fibre laser with anomalous dispersion cavity.
Chain Length Effect on Photocurrent from Polymethylene-Linked Porphyrins in Self-Assembled Monolayers (1998)

Disulfides, with a series of alkyl spacers containing porphyrins at both ends, were prepared to evaluate the effect of the spacer length on the interfacial structure and photoelectrochemical properties of self-assembled monolayers (SAMs) on a gold electrode. The structure of the SAMs was investigated using UV−visible absorption spectroscopy, cyclic voltammetry, and photoelectrochemical studies. These measurements showed that as the length of the spacers increases, the SAMs tend to form a highly ordered structure on the gold electrode. Photoelectrochemical studies, using modified Au and Pt electrodes, were carried out in the presence of methyl viologen as an electron carrier. The photocurrents decrease dramatically with a decrease in the spacer length, indicating that there are two competitive deactivation pathways for the excited porphyrin, i.e., the quenching by the electrode and electron carrier.
Survey of ribose ring pucker of signaling nucleosides and nucleotides (2020)

The ribose conformation (or puckering) of nucleosides and nucleotides is specified by two mathematical parameters describing the angular twist (phase angle, reflecting five dihedral angles) and the degree of deformation from the plane, which are represented in a pseudorotational cycle. We are interested in the ‘purinergic’ signaling role of nucleosides and nucleotides, and now many
Bilayers in 4-iodo-<i>N</i>-(2-iodo-4-nitrophenyl)benzamide generated by a combination of an N—H...O=C hydrogen bond and two independent iodo–nitro interactions (2003)

Molecules of the title compound, C(13)H(8)I(2)N(2)O(3), are linked into C(4) chains by a single N-H...O=C hydrogen bond [H...O = 2.10 A, N...O = 2.832 (5) A and N-H...O = 140 degrees ]. Two independent two-centre iodo-nitro interactions, both involving the same O atom but different I atoms [I...O = 3.205 (3) and 3.400 (3) A, and C-I...O = 160.4 (2) and 155.7 (2) degrees ], link the hydrogen-bonded chains into bilayers.
“I just went into it assuming that I wouldn't be able to have the full experience” (2020)

Virtual reality (VR) has the potential to transform many aspects of our daily lives, including work, entertainment, communication, and education. However, there has been little research into understanding the usability of VR for people with mobility limitations. In this paper, we present the results of an exploration to understand the accessibility of VR for people with limited mobility. We conducted semi-structured interviews with 16 people with limited mobility about their thoughts on, and experiences with, VR systems. We identified 7 barriers related to the physical accessibility of VR devices that people with limited mobility might encounter, ranging from the initial setup of a VR system to keeping VR controllers in view of cameras embedded in VR headsets. We also elicited potential improvements to VR systems that would address some accessibility concerns. Based on our findings, we discuss the importance of considering the abilities of people with limited mobility when designing VR systems, as the abilities of many participants did not match the assumptions embedded in the design of current VR systems.
Echocardiographic view and feature selection for the estimation of the response to CRT (2021)

Cardiac resynchronization therapy (CRT) is an implant-based therapy applied to patients with a specific heart failure (HF) profile. The identification of patients that may benefit from CRT is a challenging task and the application of current guidelines still induce a non-responder rate of about 30%. Several studies have shown that the assessment of left ventricular (LV) mechanics by speckle tracking echocardiography can provide useful information for CRT patient selection. A comprehensive evaluation of LV mechanics is normally performed using three different echocardioraphic views: 4, 3 or 2-chamber views. The aim of this study is to estimate the relative importance of strain-based features extracted from these three views, for the estimation of CRT response. Several features were extracted from the longitudinal strain curves of 130 patients and different methods of feature selection (out-of-bag random forest, wrapping and filtering) have been applied. Results show that more than 50% of the 20 most important features are calculated from the 4-chamber view. Although features from the 2- and 3-chamber views are less represented in the most important features, some of the former have been identified to provide complementary information. A thorough analysis and interpretation of the most informative features is also provided, as a first step towards the construction of a machine-learning chain for an improved selection of CRT candidates.
Process of Membership in Asynchronous Environments (1993)

The development of reliable distributed software is simplified by the ability to assume a fail-stop failure model. The emulation of such a model in an asynchronous distributed environment is discussed. The solution proposed, called Strong-GMP, can be supported through a highly efficient protocol, and was implemented as part of a distributed systems software project at Cornell University. The precise definition of the problem, the protocol, correctness proofs, and an analysis of costs are addressed.
Hydrogen adsorption on phosphorus-rich<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mo>(</mml:mo><mml:mn>2</mml:mn><mml:mn/><mml:mo>×</mml:mo><mml:mn>1</mml:mn><mml:mo>)</mml:mo></mml:math>indium phosphide (001) (2002)

Hydrogen adsorption on the InP $(001)\ensuremath{-}(2\ifmmode\times\else\texttimes\fi{}1)$ reconstruction has been characterized by vibrational spectroscopy and ab initio calculations with density functional theory. The $(2\ifmmode\times\else\texttimes\fi{}1)$ surface is covered with a complete layer of phosphorus dimers. The clean and hydrogen-terminated dimers have been modeled by ${\mathrm{In}}_{5}{\mathrm{P}}_{4}{\mathrm{H}}_{x}$ clusters with the proper number of covalent and dative bonds to accurately represent the surface of interest. The optimized molecular cluster of the unreacted dimer reveals that it has one filled and one partially filled dangling bond. Hydrogen atoms attack the P-P dimers forming terminal and coupled phosphorus-hydrogen bonds, and the predicted vibrational frequencies of these species are in excellent agreement with the infrared spectra. All the observed vibrational modes can be assigned to species containing one, two, and three hydrogen bonds (i.e., PH, HP-PH, and $\mathrm{PH}+{\mathrm{PH}}_{2})$ per surface dimer.
Essential role for a heterogeneous nuclear ribonucleoprotein (hnRNP) in oogenesis: hrp40 is absent from the germ line in the dorsoventral mutant squid. (1994)

The Drosophila melanogaster hrp40 proteins are abundant nuclear pre-mRNA-binding proteins that are similar to the heterogeneous nuclear ribonucleoprotein (hnRNP) A/B proteins of vertebrates. Recently, hrp40 has been shown to be encoded by the squid gene, which is required for dorsoventral axis formation during oogenesis. Eggs and embryos from homozygous squid mothers are severely dorsalized, and complete deletion of the squid gene results in lethality. Here we have examined the expression and localization of hrp40 in wild-type and squid mutant ovaries. Using a monoclonal antibody specific for hrp40, the same isoforms of hrp40 are detected in both wild-type and squid ovaries, but the amount of hrp40 is reduced in squid ovaries. Furthermore, immunolocalization of hrp40 in wild-type egg chambers shows that hrp40 is present in the nurse cells, oocyte, and follicle cells. In contrast, in squid mutant egg chambers, hrp40 is absent from the germ-line-derived nurse cells and oocyte, but it is detected in the somatic follicle cells. The absence of hrp40 from the germ-line-derived cells of developing egg chambers is likely to lead to the striking dorsalized phenotype of squid eggs. In addition, dramatic stage-specific changes in the cellular localization of hrp40 are seen; the protein found in the nurse cell nuclei during early stages of oogenesis migrates to the cytoplasm at later stages. These findings reveal dynamic patterns of expression and localization of hnRNP proteins during development and provide evidence for an essential role for hnRNP proteins.
Variations-aware low-power design with voltage scaling (2005)

We present a new methodology which takes into consideration the effect of Within-Die (WID) process variations on a low-voltage parallel system. We show that in the presence of process variations one should use a higher supply voltage than would otherwise be predicted to minimize the power consumption of a parallel systems. Previous analyses, which ignored WID process variations, provide a lower non-optimal supply voltage which can underestimate the energy/ operation by 8.2X. We also present a novel technique to limit the effect of temperature variations in a parallel system. As temperatures increases, the scheme reduces the power increase by 43% allowing the system to remain at it's optimal supply voltage across different temperatures.
GENOME-WIDE ASSOCIATION STUDY FOR PHARMACOGENETIC RESPONSE OF BLOOD PRESURE TO BETA BLOCKER AND CALCIUM CHANNEL BLOCKER DRUGS (2021)

Objective: There is substantial inter-individual variability in blood pressure (BP) responses to anti-hypertensive drugs and it is hypothesised that there could be genetic influences. One goal of pharmacogenetics is to aid in treatment selection. However very few variants have been identified. After the success of genome-wide association studies (GWAS) for BP, it is hoped GWAS could also reveal genes associated with BP treatment response. Design and method: A discovery analysis was performed including participants from ASCOT and NORDIL studies. Six different analyses were performed for systolic BP (SBP), diastolic BP (DBP) and pulse pressure (PP) responses to monotherapy beta blockers (BBs) and calcium channel blockers (CCBs). BP response was defined as post-treatment BP minus baseline BP. All analyses adjusted for age, sex, baseline BP and principal components. ASCOT analyses were also adjusted for dose and previous antihypertensive use, and excluded patients taking either BB/CCB drug at baseline, whereas NORDIL participants were previously untreated and subsequently treated on the same drug dose. Genotyped data was imputed to 1000 Genomes, testing ∼7million common variants. Results from ASCOT and NORDIL were meta-analysed, with total N = 2,556 for BBs and N = 3,369 for CCBs. Any variants reaching P &lt; 1 × 10-5 for SBP and DBP response to BBs were tested for replication in available ICAPS consortium data (N = 1,328). Results: Strong correlation between baseline BP and BP response shows patients with higher BP have greater BP reduction post-treatment. No variants reached genome-wide significance in any of the GWAS analyses, and none replicated in ICAPS data. Lookups of ∼1,000 published BP-associated variants were performed, but none reached Bonferroni significance level. Ongoing analyses are testing BP genetic risk scores for association with treatment response. Comparison of GWAS results shows correlation between SBP vs DBP response (r 2 = 0.48) and SBP vs PP response (r 2 = 0.76), but none between response to BBs vs CCBs. Conclusions: Despite being the largest GWAS of antihypertensive response, we found no significant associations, showing that larger studies are still required to increase power for discoveries. Model comparisons show different genes are likely to influence response to different antihypertensive drugs, with different genetic architecture.
Predictors of response to TNF antagonists in patients with ankylosing spondylitis and psoriatic arthritis: systematic review and meta-analysis (2015)

Young age, male sex, high baseline BASDAI, low baseline BASFI, high baseline CRP and HLA-B27 predict better response to TNF antagonists in AS but not in PsA.
SGBR: A Routing Protocol for Delay Tolerant Networks Using Social Grouping (2012)

Delay tolerant networks (DTN) are characterized by a lack of continuous end-to-end connections due to node mobility, constrained power sources, and limited data storage space of some or all of its nodes. To overcome the frequent disconnections, DTN nodes are required to store data packets for long periods of time until they come near other nodes. Moreover, to increase the delivery probability, they spread multiple copies of the same packet on the network so that one of them reaches the destination. Given the limited storage and energy resources of many DTN nodes, there is a tradeoff between maximizing delivery and minimizing storage and energy consumption. In this paper, we study the routing problem in DTN with limited resources. We formulate a mathematical model for optimal routing, assuming the presence of a global observer that can collect information about all the nodes in the network. Next, we propose a new protocol based on social grouping among the nodes to maximize data delivery while minimizing network overhead by efficiently spreading the packet copies in the network. We compare the new protocol with the optimal results and the existing well-known routing protocols using real life simulations. Results show that the proposed protocol achieves higher delivery ratio and less average delay compared to other protocols with significant reduction in network overhead.