gebhart/patrepeval huggingface dataset:
Bacillus Calmette-Guérin Packaged for Percutaneous Vaccination Can Be Safely Used for Intravesical Instillation in Patients with Urothelial Carcinoma of the Bladder (2020)

Intravesical instillation of percutaneous bacillus Calmette-Guérin appears to be a safe alternative to intravesical bacillus Calmette-Guérin during times of shortage. Development of additional strains, use of alternative intravesical therapies and incentivizing bacillus Calmette-Guérin production through policy change and/or alternative funding may also help avoid bacillus Calmette-Guérin supply shortages in the future.
Polycyanurate Networks with Enhanced Segmental Flexibility and Outstanding Thermochemical Stability (2012)

The synthesis and physical properties of cyanurate networks formed from two new tricyanate monomers, 1,3,5-tris[(4-cyanatophenylmethyl]benzene and 3,5-bis[(4-cyanatophenylmethyl)]phenylcyanate, are reported and compared to those of 1,1,1-tris[(4-cyanatophenyl)]ethane (also known as ESR-255). All three networks possessed somewhat different aromatic contents and cross-link densities; however, the thermochemical stability of these networks, as determined by TGA, was outstanding, with that of 1,3,5-tris[(4-cyanatophenylmethyl)]benzene being among the best known for organic cyanate esters despite its comparatively high segmental flexibility. Moreover, the moisture uptake of cured 1,3,5-tris[(4-cyanatophenylmethyl)]benzene, at 2.2% after 96 h immersed in 85 °C water, was comparatively low for a cyanate ester network with a glass transition temperature of 320 °C at full cure. When cured for 24 h at 210 °C, the dry glass transition temperatures of the networks ranged from 245 to 285 °C, while the wet glass transition temperatures ranged from 225 to 240 °C. The similarity in glass transition temperatures resulted from a lower extent of cure in the networks with more rigid segments. In essence, for networks with very high glass transition temperatures at full cure, the process conditions, rather than the rigidity of the network, determined the attainable glass transition temperature. Because networks with a higher extent of cure tend to exhibit slower long-term degradation, in this case, the networks with greater segment flexibility enabled superior performance despite exhibiting a lower glass transition temperature at full cure. These results illustrate that, in contrast to the prevailing heuristics for improving the performance of high-temperature thermosetting polymer networks, a more flexible network with a lower glass transition temperature at full cure can offer an optimal combination of thermomechanical and thermochemical performance.
Multiuser Interference in TH-UWB (2005)

Introduction Motivations and Goals Description TH-UWB Receiver Architecture
Substantial Morbidity for Hospitalized Children With Community-Acquired Rotavirus Infections (2010)

We describe community-acquired rotavirus illness in 1359 children hospitalized at 12 centers in Canada between January 2005 and December 2007. The median age was 1.5 years. Almost half (48.6%) had significant dehydration, almost one-fifth (19%) had clinical sepsis and 7% had seizures at presentation. The median hospital stay was 3.4 days. Severe clinical presentations are less commonly described in surveillance programs.
HTTP-based scalable video streaming over mobile networks (2011)

This paper proposes an adaptive HTTP-based video streaming framework for mobile networks using the Scalable Video Coding (SVC) extension to the H.264 standard. We present a method to statistically estimate the channel at the mobile client and use it in our work to adapt the bit rate of the video. The adaptation takes into account both the quality contributions and the probability of successful timely decoding for different video segments. The simulation results show significant improvements in terms of a reduction of playback interruptions and improved perceived quality of service.
Sulfamic acid catalyzed one-pot, three-component green approach: synthesis and cytotoxic evaluation of pyrazolyl-thiazole congeners (2017)

A one-pot multi-component protocol has been developed for the synthesis of biologically important pyrazolyl-thiazoles using sulfamic acid as a green catalyst in water.
Advanced MTJ Stack Engineering of STT-MRAM to Realize High Speed Applications (2020)

We demonstrate superior data retention of 1 month at 125°C with improved switching efficiency at 10 ns write time without back-hopping failure. The 40Mb macro having the advanced MTJ stacks show wide operating temperature range from -40 to 125°C with the read margin even up to 150°C and zero fail bit count with ECC on. Our study indicates that the tight switching voltage distribution and the coherent switching are essential not only for fast switching but also back-hopping margin improvement. Furthermore, our paper shows an engineering pathway how advanced MTJ stack engineering can improve key device parameters.
Variation in TRMT11 gene as a prognostic marker in advanced-stage castrate-resistant prostate cancer (CRPC) patients. (2015)

e16114 Background: In a prior study, we found that 8 single nucleotide polymorphisms (SNPs) from 4 candidate hormone-related genes (JAK2, TRMT11, NKX3-1 and HSD17B12) were associated with overall survival (OS) in CRPC stage in a North American cohort of 519 subjects. We attempt to replicate these findings in an independent cohort of Portuguese patients. Methods: A hundred and forty CRPC stage patients in the new cohort were genotyped for the candidate SNPs. The primary endpoint was overall survival (OS), defined as time from development of CRPC to death. For SNP level results we estimated hazard ratios (HR) and 95% confidence intervals (CI) under the dominant allele model using Cox regression and adjusted for age and Gleason score (GS). Results: The median age of the Portuguese cohort was 69 years (range 53-84). The GS distribution was 48% subjects with GS ≥ 8; 35% with GS = 7 and 17% with GS < 7. Median time from castration resistance to death for the cohort was 2.2 years (IQ range: 0.8-3.4, 93 deaths). One of the 3 SNPs (rs2295005; C > G; MAF = 0.16) in the TRMT11 gene was associated with OS after adjustment for age and GS: (dominant model p = 0.05, HR = 0.56; 95 CI = 0.31-1.00). No other SNP was observed to have statistical significance with OS (Table). Conclusions: Variation in the TRMT11 gene is significantly associated with overall survival in patients with CRPC and warrants further validation as a potential prognostic biomarker. SNP Gene HR ( C.I.) Adjusted p-value rs2295005 TRMT11 0.55 (0.30-1.00) 0.05 rs1268121 TRMT11 1.41 (0.87-2.28) 0.15 rs9388462 TRMT11 1.47 (0.82-2.61) 0.19 rs7005368 NKX3.1 0.94 (0.49-1.82) 0.87 rs11037662 HSD17B12 1.24 (0.74-2.08) 0.4 rs437063 JAK2 1.14 (0.69-1.88) 0.58 rs10503733 NKX3.1 1.06 (0.67-1.68) 0.79 rs3808850 JAK2 0.98 (0.62-1.53) 0.93
Resilient Living Materials Built By Printing Bacterial Spores (2019)

Abstract A route to advanced multifunctional materials is to embed them with living cells that can perform sensing, chemical production, energy scavenging, and actuation. A challenge in realizing this potential is that the conditions for keeping cells alive are not conducive to materials processing and require a continuous source of water and nutrients. Here, we present a 3D printer that can mix material and cell streams in a novel printhead and build 3D objects (up to 2.5 cm by 1 cm by 1 cm). Hydrogels are printed using 5% agarose, which has a low melting temperature (65°C) consistent with thermophilic cells, a rigid storage modulus (G’= 6.5 × 10 4 ), exhibits shear thinning, and can be rapidly hardened upon cooling to preserve structural features. Spores of B. subtilis are printed within the material and germinate on its exterior, including spontaneously in cracks and new surfaces exposed by tears. By introducing genetically engineered bacteria, the materials can sense chemicals (IPTG, xylose, or vanillic acid). Further, we show that the spores are resilient to extreme environmental stresses, including desiccation, solvents (ethanol), high osmolarity (1.5 mM NaCl), 365 nm UV light, and γ-radiation (2.6 kGy). The construction of 3D printed materials containing spores enables the living functions to be used for applications that require long-term storage, in-field functionality, or exposure to uncertain environmental stresses.
Characterization and performance of short cationic antimicrobial peptide isomers (2013)

Cationic antimicrobial peptides (CAMPs) represent an ancient defense mechanism against invading bacteria, with peptides such as the cathelicidins being essential elements of vertebrate innate immunity. CAMPs are typically associated with broad-spectrum antimicrobial potency and limited bacterial resistance. The cathelicidin identified from the elapid snake Naja atra (NA-CATH) contains a semi-conserved repeated 11-residue motif (ATRA motif) with a sequence pattern consistent with formation of an amphipathic helical conformation. Short peptide amides (ATRA-1, -1A, -1P, and -2) generated based on the pair of ATRA motifs in NA-CATH exhibited varied antimicrobial potencies. The small size of the ATRA peptides, coupled with their varied antimicrobial performances, make them interesting models to study the impact various physico-chemical properties have on antimicrobial performance in helical CAMPs. Accordingly, the D- and L-enantiomers of the peptide ATRA-1A, which in earlier studies had shown both good antimicrobial performance and strong helical character, were investigated in order to assess the impact peptide stereochemistry has on antimicrobial performance and interaction with chiral membranes. The ATRA-1A isomers exhibit varied potencies against four bacterial strains, and their conformational properties in the presence of mixed zwitterionic/anionic liposomes are influenced by anionic lipid content. These studies reveal subtle differences in the properties of the peptide isomers. Differences are also seen in the abilities of the ATRA-1A isomers to induce liposome fusion/aggregation, bilayer rearrangement and lysing through turbidity studies and fluorescence microscopy. The similarities and differences in the properties of the ATRA-1A isomers could aid in efforts to develop D-peptide-based therapeutics using high-performing L-peptides as templates.
Replicated Softmax: an Undirected Topic Model (2009)

We introduce a two-layer undirected graphical model, called a Replicated Softmax, that can be used to model and automatically extract low-dimensional latent semantic representations from a large unstructured collection of documents. We present efficient learning and inference algorithms for this model, and show how a Monte-Carlo based method, Annealed Importance Sampling, can be used to produce an accurate estimate of the log-probability the model assigns to test data. This allows us to demonstrate that the proposed model is able to generalize much better compared to Latent Dirichlet Allocation in terms of both the log-probability of held-out documents and the retrieval accuracy.
Abstract 730: Genomic characterization of hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a rare and aggressive kidney cancer (2019)

BackgroundHereditary Leiomyomatosis and Renal Cell Carcinoma (HLRCC) is a rare autosomal-dominant syndromic disorder associated with germline FH mutations. Affected individuals have a predisposition to cutaneous and uterine leiomyoma’s, and are at increased risk of developing a renal cell carcinoma (HLRCC- associated RCC) with aggressive clinical outcome. However, aside from FH bi-allelic loss, additional genomic features of HLRCC are currently poorly understood.MethodFive cases of HLRCC-associated RCC were characterized using integrated next generation sequencing (NGS) technology. This included an index case where multiple tumor sites (kidney, lung, liver, lymph node, skin, and uterine) from a single patient were characterized. For integrative analysis, in-house data were combined with five RCC cases with FH bi-allelic loss from The Cancer Genome Atlas Study. Single cell sequencing was carried out on normal human kidney to study the cell of origin for HLRCC- associated RCC.Results: Integrative NGS profiling and analysis of HLRCC-associated RCC tumors (n=10) revealed several important observations such as 1) a high frequency loss of whole chromosomes, which is reminiscent of tumors arising from the distal nephron, 2) low mutational burden similar to that observed in other kidney tumors and, 3) a HLRCC specific gene expression signature and discovery of a novel therapeutic candidate (HLRCC-TC1). Importantly, among renal tumors, HLRCC-TC1 was specifically expressed in HLRCC and other RCCs with poor clinical outcome. Application of siRNAs and neutralizing antibodies to HLRCC-TC1 reduced cell proliferation of the HLRCC cell line UOK262, but did not for that of control cell lines.Conclusion: The observed FH bi-allelic mutation along with recurrent chromosome-wide losses and integrative analysis with human kidney single cell sequencing data support a distal nephron origin for HLRCC- associated RCC. In addition, our study provides evidence for nominating HLRCC-TC1 as a novel cancer-specific therapeutic target. Further studies are needed to conduct an in-depth characterization of HLRCC-TC1.Citation Format: Pankaj Vats, Yuping Zhang, Sarvana Mohan Dhanashekaran, Narayanan Sathiya Pandi, Xuhong Cao, Fengyun Su, Sudhanshu Shukla, Rui Wang, Marcin Cieslik, Jincheng Pan, Christopher J. Ricketts, Prem Kumar Kumpati, Ajjai Alva, Marston W. Linehan, Rohit Mehra, Arul M. Chinnaiyan. Genomic characterization of hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a rare and aggressive kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 730.
Activation of the Calcium Sensing Receptor (casr) Prevents Secretagogue-Induced Diarrhea in the Rat Small Intestine (2018)

Introduction Diarrhea is still a leading cause of death in children and the elderly worldwide, especially during antibiotic therapy in transplant/immunosuppressed patients. The incidence and the severity of diarrhea has been reduced using oral rehydration solution (ORS), but it does not directly reduce intestinal secretion and may paradoxically worsen diarrhea. Consequently, new alternative anti-diarrheal therapies are needed. The calcium-sensing receptor (CaSR) is localized in numerous body tissues, but its function in the small intestine and in the colon, is still not clear. Fluid and electrolyte homeostasis (secretion and absorption) is controlled primarily in the intestine. We demonstrate the function of the CaSR in the small intestine and the colon using calcium and calcium nanoparticles solution to activate the intestinal CaSR and prevent cyclic nucleotide-induced diarrhea. Materials and methods Male Sprague-Dawley rats’ small intestinal and colon segments were isolated and connected into an ex vivo bowel perfusion device. Extraluminally, the segments were perfused with HEPES buffer. Intraluminally, the small intestines were perfused with different concentrations of calcium (1.0, 5.0, and 7.0 mM) and the colon segments were perfused with and without calcium nanoparticles. The experiments were conducted both in presence and absence of Forskolin, a potent secretagogue. Secretory-absorptive function was assessed based on nanospectrophotometric measurements of FITC-Inulin, a non-absorbable fluorescent marker bound to a biologically inert sugar. Results and Discussion Elevated levels of luminal calcium perfusion reduced intestinal secretion, and, at higher concentrations, led to moderate absorption. Elevation of the luminal calcium concentration to 7.0 mM abolished the classical Forskolin-induced secretion. The 7.0 mM calcium-perfusate demonstrated enhanced absorption from the proximal to distal portions of the small intestine, with an approximate two-fold increase in the absorptive rate when compared to the proximal and distal small intestine perfusated with 1.0 mM and 5.0 mM of calcium. In the colon, the Forskolin perfusion rapidly induced considerable secretion. The addition of calcium nanoparticles to the perfusate resulted in a return to a normal secretion profile, indicating prevention/abatement of cyclic nucleotide-induced diarrhea. Conclusion The present study provides evidence of the functional activity of apical CaSR from the proximal to the distal portions of the small intestine and the colon segments. Furthermore, CaSR activation through calcium nanoparticles abates Forskolin induced fluid secretion and can lead to absorption of fluid at higher concentrations, despite continued presence of the cyclic nucleotide activator. Calcium and calcium nanoparticles can mitigate secretagogue-induced diarrhea. These results suggest that the use of nanoparticles may be a potential treatment or a prophylactic therapy of diarrhea.
Principle and applications of an autocharge-compensated sample and hold circuit (1995)

This paper describes an autocharge-compensated sample and hold circuit (ACC-SH) for thin film transistor active matrix liquid-crystal displays (TFT-AM-LCD's, TFT-LCD's, or LCD's). The operating principle and actual application problems for TFT-LCD's are also discussed. The applicability of the ACC-SH is verified not only by circuit simulation but also by experimental circuit die measurement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A linear programming approach to bounding spectral power (2005)

The mapping from a finite set of correlation samples to a power density spectrum is not unique. Furthermore, power density spectra exist that take on arbitrary values at a particular frequency and yet are consistent with the correlation samples. Thus values of the spectral density function at a particular frequency cannot be determined without further prior information. In a recent paper, Cybenko comments that tight upper and lower bounds on linear functionals of the spectral density can be obtained as solutions of semi-infinite linear programming problems. In this paper, the primal linear programming problem is interpreted as a search for extremal spectra and the dual linear programming problem is interpreted as a data-adaptive window design procedure. The effect of discretization on both the primal and dual problems is noted. Finally, it is shown how the dual window design problem can be used to design fixed classical type windows for the computation of suboptimal bounds.
Rh-catalyzed reagent-free ring expansion of cyclobutenones and benzocyclobutenones (2015)

Here we report a reagent-free rhodium-catalyzed ring-expansion reaction via C-C cleavage of cyclobutenones. A variety of poly-substituted cyclopentenones and 1-indanones can be synthesized from simple cyclobutenones and benzocyclobutenones. The reaction condition is near pH neutral without additional oxidants or reductants. The potential for developing a dynamic kinetic asymmetric transformation of this reaction has also been demonstrated. Further study supports the proposed pathway involving Rh-insertion into the cyclobutenone C-C bond, followed by β-hydrogen elimination, olefin insertion and reductive elimination.
A study on the common mode current generated from an AFE of a modem and the magnetic field emitted from signal wires driven by the AFE (2008)

The common mode current generated by an AFE (analog-front-end) of a modem is a main cause of emission from the external wires connected with the AFE. In this paper, the measurement and the calculation are carried out about the common mode current and the magnetic field generated from the AFE by the equivalent circuit that consists of a signal generator and an output transformer. As a result, it is confirmed by the calculation and the measurement that the common mode current increases according to the coupling capacitances between the primary and the secondary windings of the output transformer and the parasitic capacitances caused by traces, and that the magnetic field strength emitted from the signal wires is proportional to the common mode current. And then, an output transformer with a balun is proposed. It is clarified that the transformer with a balun is effective to reduce the common mode current and the magnetic field.
Abstract SY01-01: Regulation of growth by the mTOR pathway. (2013)

Abstract mTOR is the target of the immunosuppressive drug rapamycin and the central component of a nutrient-and hormone-sensitive signaling pathway that regulates cell growth and proliferation. We now appreciate that this pathway becomes deregulated in many human cancers and has an important role in the control of metabolism and aging. We have identified two distinct mTOR-containing proteins complexes, one of which regulates growth through S6K and another that regulates cell survival through Akt. These complexes, mTORC1 and mTORC2, define both rapamycin-sensitive and insensitive branches of the mTOR pathway. I will discuss new results from our lab on the regulation and functions of the mTORC1 and mTORC2 pathways. Citation Format: David M. Sabatini. Regulation of growth by the mTOR pathway. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY01-01. doi:10.1158/1538-7445.AM2013-SY01-01
Resistive switching and data reliability of epitaxial (Ba,Sr)TiO3 thin films (2006)

We report on resistive switching of capacitor-like SrRuO3∕Ba0.7Sr0.3TiO3∕Pt thin films epitaxially grown on SrTiO3 substrates. We observe a weak but stable hysteresis in the current-voltage curve. By applying short voltage pulses, a high or low resistive state as well as intermediate states can be addressed even at room temperature. We demonstrate a multiple-branch hysteresis curve corresponding to multilevel switching modus revealing different subloops for different write voltages. Furthermore reliability issues such as cycling endurance and data retention are presented. Read-write operations over 10000cycles show a fatigue-like drift of both resistance states. No data loss is found upon continuous readout.
Entropy-SGD: Biasing Gradient Descent Into Wide Valleys (2016)

This paper proposes a new optimization algorithm called Entropy-SGD for training deep neural networks that is motivated by the local geometry of the energy landscape. Local extrema with low generalization error have a large proportion of almost-zero eigenvalues in the Hessian with very few positive or negative eigenvalues. We leverage upon this observation to construct a local-entropy-based objective function that favors well-generalizable solutions lying in large flat regions of the energy landscape, while avoiding poorly-generalizable solutions located in the sharp valleys. Conceptually, our algorithm resembles two nested loops of SGD where we use Langevin dynamics in the inner loop to compute the gradient of the local entropy before each update of the weights. We show that the new objective has a smoother energy landscape and show improved generalization over SGD using uniform stability, under certain assumptions. Our experiments on convolutional and recurrent networks demonstrate that Entropy-SGD compares favorably to state-of-the-art techniques in terms of generalization error and training time.
Interleukin-1 Receptor Blockade Is Associated With Reduced Mortality in Sepsis Patients With Features of Macrophage Activation Syndrome (2015)

In this subgroup analysis, interleukin-1 receptor blockade was associated with significant improvement in survival of patients with sepsis and concurrent hepatobiliary dysfunction/disseminated intravascular coagulation. A prospective randomized trial using features of macrophage activation syndrome for mortality risk stratification should be undertaken to confirm the role of interleukin-1 blockage.