gebhart/patrepeval huggingface dataset:
The meniscus on a needle – a lesson in matching (1983)

We reconsider the second approximation for the height of the meniscus on a slender vertical cylinder, which has been calculated by James using the method of matched asymptotic expansions. Fraenkel has warned that the asymptotic matching principle may fail in certain cases, and we confirm that failure here. This meniscus problem is used to discuss the kind of failures that may occur if Fraenkel's restricted form of the matching principle is not used. A less restricted matching principle is also suggested in this paper. With this matching principle, we show that the last known term of order Re 3 In Re in the drag on a sphere in low-Reynolds-number flow is correct, even though it was found in a way that violates Fraenkel's warning.
Men Who have Sex with Men in China have Relatively Low Numbers of Sexual Partners (2011)

HIV prevalence is increasing rapidly among men who have sex with men (MSM) in China and potentially associated with the number of male sexual partners that each man has on average. This study estimates the distribution of the number of male sexual partners among Chinese MSM through a comprehensive review of English and Chinese published literature. The overall median number of male sexual partners of Chinese MSM in the past 6 months China was estimated to be 1.5 (95% CI, 1.1-1.8) and 3.8 (95% CI 1.5-6.9) sexual partners in the past 6-month and 12-month periods respectively. An estimated 31% of sexual partners of MSM in China are regular partners, 54% are casual partners, and 16% are commercial partners. The reported numbers of sexual partners has not changed over time during the past decade. The numbers of male sexual partners reported by Chinese MSM is consistently lower than other settings and may not be sufficient to explain the recent rapid increase in HIV prevalence.
Hardware validated unified model of multibit temporally and spatially oversampled image sensors with conditional reset (2014)

We describe a photon statistics-based theoretical model of the response to incident light of an image sensor and show that conditional reset and multibit temporal oversampling increase the dynamic range significantly. This photon-based modeling approach describes the full image sensor design space of temporal and spatial oversampling either with a binary comparison or with a multibit read of each sample. We find excellent quantitative agreement between measurements on custom hardware and our theoretical predictions. We then use this model to show what improvements in dynamic range and low-light response can be achieved by oversampling and what the limits of improvement caused by pixel size and lens parameters are.
pH-Sensitive Liposomes for Enhanced Cellular Uptake and Cytotoxicity of Daunorubicin in Melanoma (B16-BL6) Cell Lines (2022)

Daunorubicin (DNR) was delivered using a pH-sensitive liposomal system in B16-BL6 melanoma cell lines for enhanced cytotoxic effects. DNR was encapsulated within liposomes and CL as a component of the lipid bilayer. PEGylated pH-sensitive liposomes, containing CL, were prepared in the molar ratio of 40:30:5:17:8 for DOPE/cholesterol/DSPE-mPEG (2000)/CL/SA using the lipid film hydration method and loaded with DNR (drug: lipid ratio of 1:5). The CL liposomes exhibited high drug encapsulation efficiency (>90%), a small size (~94 nm), narrow size distribution (polydispersity index ~0.16), and a rapid release profile at acidic pH (within 1 h). Furthermore, the CL liposomes exhibited 12.5- and 2.5-fold higher cytotoxicity compared to DNR or liposomes similar to DaunoXome®. This study provides a basis for developing DNR pH-sensitive liposomes for melanoma treatment.
Genome Sequence and Analysis ofEscherichia coliMRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI (2016)

Escherichia coli strain MRE600 was originally identified for its low RNase I activity and has therefore been widely adopted by the biomedical research community as a preferred source for the expression and purification of transfer RNAs and ribosomes. Despite its widespread use, surprisingly little information about its genome or genetic content exists. Here, we present the first de novo assembly and description of the MRE600 genome and epigenome. To provide context to these studies of MRE600, we include comparative analyses with E. coli K-12 MG1655 (K12). Pacific Biosciences Single Molecule, Real-Time sequencing reads were assembled into one large chromosome (4.83 Mb) and three smaller plasmids (89.1, 56.9, and 7.1 kb). Interestingly, the 7.1-kb plasmid possesses genes encoding a colicin E1 protein and its associated immunity protein. The MRE600 genome has a G + C content of 50.8% and contains a total of 5,181 genes, including 4,913 protein-encoding genes and 268 RNA genes. We identified 41,469 modified DNA bases (0.83% of total) and found that MRE600 lacks the gene for type I methyltransferase, EcoKI. Phylogenetic, taxonomic, and genetic analyses demonstrate that MRE600 is a divergent E. coli strain that displays features of the closely related genus, Shigella. Nevertheless, comparative analyses between MRE600 and E. coli K12 show that these two strains exhibit nearly identical ribosomal proteins, ribosomal RNAs, and highly homologous tRNA species. Substantiating prior suggestions that MRE600 lacks RNase I activity, the RNase I-encoding gene, rna, contains a single premature stop codon early in its open-reading frame.
Identification of cyclic AMP phosphodiesterases 3, 4 and 7 in human CD4+and CD8+T‐lymphocytes: role in regulating proliferation and the biosynthesis of interleukin‐2 (1996)

1. The cyclic AMP phosphodiesterases (PDE) expressed by CD4+ and CD8+ T-lymphocytes purified from the peripheral blood of normal adult subjects were identified and characterized, and their role in modulating proliferation and the biosynthesis of interleukin (IL)-2 and interferon (IFN)-gamma evaluated. 2. In lysates prepared from both subsets, SK&F 95654 (PDE3 inhibitor) and rolipram (PDE4 inhibitor) suppressed cyclic AMP hydrolysis indicating the presence of PDE3 and PDE4 isoenzymes in these cells. Differential centrifugation and subsequent inhibitor and kinetic studies revealed that the particulate fraction contained, predominantly, a PDE3 isoenzyme. In contrast, the soluble fraction contained a PDE4 (approximately 65% of total activity) and, in addition, a novel enzyme that had the kinetic characteristics of the recently identified PDE7. 3. Reverse transcription-polymerase chain reaction (RT-PCR) studies with primer pairs designed to recognise unique sequences in the human PDE4 and PDE7 genes amplified cDNA fragments that corresponded to the predicted sizes of HSPDE4A, HSPDE4B, HSPDE54D and HSPDE7. No message was detected for HSPDE4C after 35 cycles of amplification. 4. Functionally, rolipram inhibited phytohaemagglutinin- (PHA) and anti-CD3-induced proliferation of CD4+ and CD8+ T-lymphocytes, and the elaboration of IL-2, which was associated with a three to four fold increase in cyclic AMP mass. In all experiments, however, rolipram was approximately 60 fold more potent at suppressing IL-2 synthesis than at inhibiting mitogenesis. In contrast, SK&F 95654 failed to suppress proliferation and cytokine generation, and did not elevate the cyclic AMP content in T-cells. Although inactive alone, SK&F 95654 potentiated the ability of rolipram to suppress PHA- and anti-CD3-induced T-cell proliferation, and PHA-induced IL-2 release. 5. When a combination of phorbol myristate acetate (PMA) and ionomycin were used as a co-mitogen, rolipram did not affect proliferation but, paradoxically, suppressed IL-2 release indicating that cyclic AMP can inhibit mitogenesis by acting at, or proximal to, the level of inositol phospholipid hydrolysis. 6. Collectively, these data suggest that PDE3 and PDE4 isoenzymes regulate the cyclic AMP content, IL-2 biosynthesis and proliferation in human CD4+ and CD8+ T-lymphocytes. However, the ability of rolipram to suppress markedly mitogen-induced IL-2 generation without affecting T-cell proliferation suggests that growth and division of T-lymphocytes may be governed by mediators in addition to IL-2. Finally, T-cells have the potential to express PDE7, although elucidating the functional role of this enzyme must await the development of selective inhibitors.
Substituted 2,5‘-Bi-1H-benzimidazoles:  Topoisomerase I Inhibition and Cytotoxicity (1996)

Several 2'-aryl-5-substituted-2,5'bi-1H-benzimidazole derivatives were synthesized and evaluated as topoisomerase I poisons and for their cytotoxicity toward the human lymphoblast cell line RPMI 8402. This study focused on 18 2,5'-bi-1H-benzimidazole derivatives which contained either a 5-cyano, a 5-(aminocarbonyl), or a 5-(4-methylpiperazinyl) group. Among these bibenzimidazoles, the pharmacological activity of 2'-phenyl derivatives and the influence of the different positional isomers of either a 2'-tolyl group or a 2'-naphthyl moiety on cytotoxicity and topoisomerase I inhibitory activity were determined.
3D mirror symmetry detection using Hough transform (2008)

This paper describes a simple and efficient means for statistical detection of global and local mirror symmetry. The symmetry planes are selected from all the planes obtained after matching and pairing features extracted on 3D meshes. The original part of the proposed method is the way to extract significant symmetry planes with a 3D Hough transform built from the planes parameters. This method generates faster results compared to existing statistical methods for symmetry detection.
Functional Correlation of GABAAReceptor α Subunits Expression with the Properties of IPSCs in the Developing Thalamus (2000)

GABA(A) receptor alpha1 and alpha2 subunits are expressed differentially with ontogenic period in the brain, but their functional roles are not known. We have recorded GABA(A) receptor-mediated IPSCs from laterodorsal (LD) thalamic relay neurons in slices of rat brain at various postnatal ages and found that decay times of evoked IPSCs and spontaneous miniature IPSCs undergo progressive shortening during the first postnatal month. With a similar time course, expression of transcripts and proteins of GABA(A) receptor alpha2 subunit in LD thalamic region declined, being replaced by those of alpha1 subunit. To further address the causal relationship between alpha subunits and IPSC decay time kinetics, we have overexpressed GABA(A) receptor alpha1 subunit together with green fluorescent protein in LD thalamic neurons in organotypic culture using recombinant Sindbis virus vectors. Miniature IPSCs recorded from the LD thalamic neurons overexpressed with alpha1 subunit had significantly faster decay time compared with control expressed with beta-galactosidase. We conclude that the alpha2-to-alpha1 subunit switch underlies the developmental speeding in the decay time of GABAergic IPSCs.
Phase II Assessment of Recombinant Leukocyte A Interferon with Difluoromethylornithine in Disseminated Malignant Melanoma (1990)

Sixteen patients with advanced melanoma received IFN-alpha 2A, 36 X 10(6) U/m2 i.m., on days 3-7 with 2.25 g/m2 DFMO p.o. on days 1-7. We observed no objective regressions. Median time to progression was 1.2 months with a median survival of 5.2 months. A flu-type syndrome was the predominant sequela. From the dose and schedule that we utilized, this regimen holds little promise against disseminated malignant melanoma.
Power efficient photonic networks on-chip (2008)

The emerging class of multicore architectures and chip multiprocessors (CMPs) has fundamentally shifted the impact of communications on computing systems performance. Global communications at all scales is playing a central and dominant role in the ultimate realization of CMP system performance as it falls increasingly on the efficiency of the information exchange among the vastly growing number of compute and memory resources. In this new communication-bound paradigm, the realization of a system-wide scalable communications infrastructure that can meet the enormous bandwidths, capacities, and stringent latency requirements in an energy efficient manner is a key goal for scaling future computation performance. We explore how recent extraordinary advances in nanoscale silicon photonic technologies can be exploited for developing optical interconnection networks that address the critical bandwidth and power challenges presented across several levels of the CMP computing system communications infrastructure. Unlike prior generations of photonic technologies, the remarkable capabilities of nanoscale "CMOS photonics" offer the possibility of creating highly integrated platforms for generating and receiving optical signals with fundamentally superior power efficiencies. Optical interconnection network architectures employing these silicon nanophotonic building blocks are uniquely co-developed and explored in the context of bandwidth-driven computing models. The design of an on-chip optical interconnection network that employs nanoscale CMOS photonic devices and enables seamless off-chip communications to other CMP computing nodes and to external memory is described.
off-State Current Limits of Narrow Bandgap MOSFETs (2006)

OFF-state current limitations of two types of MOSFETs, namely 1) flatband-mode MOSFET and 2) inversion-mode MOSFET, with narrow bandgap channel materials such as InSb, InAs, InGaAs, and Ge are discussed in conjunction with long-term requirements of the International Technology Roadmap for Semiconductors (ITRS). Flatband-mode high-mobility MOSFETs appear to be better suited for low off-state currents, in particular when a backside contact is used for minority carrier extraction. Based on off-state thermal minority carrier generation in narrow bandgap materials at room temperature, flatband MOSFETs with InSb channels appear to be applicable for high-performance logic and even low operating power requirements of the long-term ITRS; however, standby power requirements will demand InAs or channels of higher bandgap unless material and interface quality (and, thus, carrier lifetime) is substantially improved. The effects of drain-induced barrier lowering, band-to-band tunneling, impact ionization, and increased temperature on off-state currents are not considered here but may impose further restrictions
Alternating hemiplegia of childhood: evolution over time and mouse model corroboration (2021)

Alternating hemiplegia of childhood is a rare neurodevelopmental disorder caused by <i>ATP1A3</i> mutations. Some evidence for disease progression exists, but there are few systematic analyses. Here, we evaluate alternating hemiplegia of childhood progression in humans and in the D801N knock-in alternating hemiplegia of childhood mouse, Mashlool, model. This study performed an ambidirectional (prospective and retrospective data) analysis of an alternating hemiplegia of childhood patient cohort (<i>n</i> = 42, age 10.24 ± 1.48 years) seen at one US centre. To investigate potential disease progression, we used linear mixed effects models incorporating early and subsequent visits, and Wilcoxon Signed Rank test comparing first and last visits. Potential early-life clinical predictors were determined via multivariable regression. We also compared EEG background at first encounter and at last follow-up. We then performed a retrospective confirmation study on a multicentre cohort of alternating hemiplegia of childhood patients from France (<i>n</i> = 52). To investigate disease progression in the Mashlool mouse, we performed behavioural testing on a cohort of Mashlool<sup>-</sup> mice at prepubescent and adult ages (<i>n</i> = 11). Results: US patients, over time, demonstrated mild worsening of non-paroxysmal disability index scores, but not of paroxysmal disability index scores. Increasing age was a predictor of worse scores: <i>P</i> < 0.0001 for the non-paroxysmal disability index, intellectual disability scale and gross motor scores. Earliest non-paroxysmal disability index score was a predictor of last visit non-paroxysmal disability index score (<i>P</i> = 0.022), and earliest intellectual disability score was a predictor of last intellectual disability score (<i>P</i> = 0.035). More patients with EEG background slowing were noted at last follow-up as compared to initial (<i>P</i> = 0.015). Similar worsening of disease with age was also noted in the French cohort: age was a significant predictor of non-paroxysmal disability index score (<i>P</i> = 0.001) and first and last non-paroxysmal disability index score scores significantly differed (<i>P</i> = 0.002). In animal studies, adult Mashlool mice had, as compared to younger Mashlool mice, (i) worse balance beam performance; (ii) wider base of support; (iii) higher severity of seizures and resultant mortality; and (iv) no increased predisposition to hemiplegic or dystonic spells. In conclusion, (i) non-paroxysmal alternating hemiplegia of childhood manifestations show, on average over time, progression associated with severity of early-life non-paroxysmal disability and age. (ii) Progression also occurs in Mashlool mice, confirming that <i>ATP1A3</i> disease can lead to age-related worsening. (iii) Clinical findings provide a basis for counselling patients and for designing therapeutic trials. Animal findings confirm a mouse model for investigation of underlying mechanisms of disease progression, and are also consistent with known mechanisms of <i>ATP1A3</i>-related neurodegeneration.
Analysis of Xanthate Derivatives by Vacuum Ultraviolet Laser-Time-of-Flight Mass Spectrometry (1998)

A series of liquid O,S-dialkyl dithiocarbonates (xanthate esters) have been synthesized, and time-of-flight (TOF) mass spectra were recorded for their vapors using both ultraviolet (UV) and vacuum ultraviolet (VUV) laser excitation. These compounds are chemical derivatives of low vapor pressure xanthate salts which have found important commercial application as collectors in mineral sulfide flotation circuits. Our experiments demonstrate that esters ionized by short-wavelength VUV light can be detected by parent mass with high efficiency and minimal fragmentation. In contrast, the mass spectra of the same compounds obtained by UV light excitation exhibit a large number of low molecular mass peaks. A preliminary quantitative analysis of the composition of a gas-phase mixture of xanthate esters has also been achieved, which indicates possible subfemtomole detection limits.
Decreased endothelium-dependent pulmonary vasodilator effect of calcitonin gene-related peptide in hypoxic rats contrasts with increased binding sites (1995)

Levels of calcitonin gene-related peptide (CGRP), a vasodilator peptide present in nerves and airway endocrine cells of the rat respiratory tract, are increased in hypoxic lung and decreased in plasma, suggesting impaired CGRP release. We wanted to determine whether there was an adaptive functional response to reduced CGRP levels in hypoxia. Density of binding sites for CGRP were compared with its vascular actions following hypoxia, and with binding following administration of the sensory neurotoxin capsaicin to deplete neural CGRP. Autoradiography of lung sections incubated with 125I-labelled CGRP and other vasoactive peptides was used to quantify their binding sites, in male Wistar rats exposed to periods of hypoxia (inspiratory oxygen fraction (FI,O2) = 0.1) ranging 0-10 days (n = 5 each), in controls, and in rats treated neonatally with capsaicin. Relaxation to CGRP was compared in pulmonary artery of control and hypoxic rats. CGRP binding was seen in the vascular endothelium and was significantly elevated after 5 days of hypoxia (mean +/- SEM: control 4.6 +/- 0.4 versus hypoxic 16.6 +/- 2.4 amol.mm-2). CGRP-induced (5 x 10(-7)M) relaxation of pulmonary artery was reduced, compared with controls, following 8 and 21 days of hypoxia (mean +/- SEM) percentage of relaxation to phenylephrine: 78 +/- 3, 36 +/- 5 and 32 +/- 3, respectively) and was abolished by removal of endothelium. Capsaicin treatment also significantly elevated vascular CGRP binding. Atrial natriuretic peptide (ANP) binding levels were decreased in smooth muscle of all blood vessels after 7 days of hypoxia, but endothelin-1 (ET-1) and vasoactive intestinal peptide (VIP) binding was unchanged. We conclude that the vasodilator effects of CGRP are endothelium-dependent and, whilst they are reduced in hypoxic lung, this is not due to reduction in receptors, thereby implicating alterations in the nitric oxide guanylyl cyclase system. Furthermore, adaptive responses in some peptide binding sites occur in hypoxia, which may be due to changes in endogenous peptide levels.
Potential Relevance ofChlamydia pneumoniaeSurface Proteins to an Effective Vaccine (2000)

The surface of Chlamydia pneumoniae is covered with proteins but their exact identification is not known probably because of the presence of conformational epitopes. A family of 21 pmp genes has been found by DNA sequencing. In common, these genes have the capacity to encode the amino acid motif GGAI. Several of the genes have the capacity to encode outer membrane proteins of about 100 kDa. Thus, they are candidate genes to encode the protein(s) present in the 98-kDa protein band of the C. pneumoniae outer membrane complex. The production of recombinant GGAI proteins is described as is the use of polyclonal antibodies raised against the recombinant GGAI proteins to determine their expression in C. pneumoniae elementary bodies. At least three of the proteins, Omp4, 5, and 11, are expressed.
Capsicum annuum transcription factor WRKYa positively regulates defense response upon TMV infection and is a substrate of CaMK1 and CaMK2 (2015)

Abstract Plants are constantly exposed to pathogens and environmental stresses. To minimize damage caused by these potentially harmful factors, plants respond by massive transcriptional reprogramming of various stress-related genes via major transcription factor families. One of the transcription factor families, WRKY, plays an important role in diverse stress response of plants and is often useful to generate genetically engineered crop plants. In this study, we carried out functional characterization of CaWRKYa encoding group I WRKY member, which is induced during hypersensitive response (HR) in hot pepper ( Capsicum annuum ) upon Tobacco mosaic virus (TMV) infection. CaWRKYa was involved in L -mediated resistance via transcriptional reprogramming of pathogenesis - related ( PR ) gene expression and affected HR upon TMV-P 0 infection. CaWRKYa acts as a positive regulator of this defense system and could bind to the W -box of diverse PR genes promoters. Furthermore, we found Capsicum annuum mitogen-activated protein kinase 1 (CaMK1) and 2 (CaMK2) interacted with CaWRKYa and phosphorylated the SP clusters but not the MAPK docking (D)-domain of CaWRKYa. Thus, these results demonstrated that CaWRKYa was regulated by CaMK1 and CaMK2 at the posttranslational level in hot pepper.
Identifying superionic conductors by materials informatics and high-throughput synthesis (2020)

Abstract Combinatorial chemistry has been proven effective in the search for novel functional materials, especially in the field of organic chemistry, and is being used to identify functional inorganic compounds. However, there is a growing need for approaches that predict and experimentally realize new materials, beyond composition optimization of known systems. Application of combinatorial chemistry to materials discovery is typically hindered by a limited ability to search a wide chemical composition space, and by our ability to experimentally screen promising compounds. Here, a combinatorial scheme is proposed that combines a materials informatics technique to define a chemical search space with high-throughput synthesis and evaluation. We identify high-performance superionic conductors in the Ca-(Nb,Ta)-Bi-O system, demonstrating the effectiveness of this approach for accelerated materials discovery.