gebhart/patrepeval huggingface dataset:
Fecal Prevalence and Diversity of Salmonella Species in Lactating Dairy Cattle in Four States (2005)

Salmonella is one of the most serious foodborne pathogenic bacteria in the United States, causing an estimated 1.3 million human illnesses each year. Dairy cows can be reservoirs of foodborne pathogenic bacteria, including Salmonella spp.; it is estimated that from 27 to 31% of dairy herds across the United States are colonized by Salmonella. The present study was designed to examine the occurrence of Salmonella spp. on dairies and to examine the serotypic diversity of Salmonella isolates on sampled dairies from across the United States. Fecal samples (n = 60 per dairy) were collected from 4 dairies in each of 4 states for a total of 960 fecal samples representing a total population of 13,200 dairy cattle. In the present study, 93 of 960 samples (9.96%) collected were culture-positive for Salmonella enterica. At least one Salmonella fecal-shedding cow was found in 9 of the 16 herds (56%) and the within-herd prevalence varied in our study from 0% in 7 herds to a maximum of 37% in 2 herds, with a mean prevalence among Salmonella-positive herds of 17%. Seventeen different serotypes were isolated, representing 7 different Salmonella serogroups. There were 2 or more different serogroups and serotypes present on 7 of the 9 Salmonella-positive farms. Serotypes Montevideo and Muenster were the most frequent and widespread. From our data, it appears that subclinical colonization with Salmonella enterica is relatively common on dairy farms and is represented by diverse serotypes on US dairy farms.
RNA secondary structure is an integral part of the in vitro mechanism of attenuation in simian virus 40 (1989)

At late times after infection with SV40, a prematurely terminated transcript that initiates at the major late promoter (MLP) and has a 3'-end about 95 nucleotides downstream has been identified and termed an attenuated RNA (Hay, N., Skolnik-David, H., and Aloni, Y. (1982) Cell 29, 183-193). The DNA template of the attenuated RNA has two regions of dyad symmetry, and the attenuated RNA can therefore fold into two hairpin elements. The hairpin element at the 3'-end of the attenuated RNA is followed by a stretch of Us and resembles a rho-independent terminator in prokaryotes. We have suggested that folding of the RNA into two hairpin elements will lead to a block of transcription elongation. Using site-directed mutagenesis, we created two templates that either strengthened or weakened the proposed hairpin structures. The mutated and wild-type templates were cloned downstream from the adenovirus 2 MLP, and transcription patterns were compared between the templates in a cell-free extract. We have shown that RNA polymerase II recognizes the SV40 sequence that leads to a block of transcription elongation, even when it is under the control of the MLP of adenovirus 2. The extent of the block of transcription elongation is directly dependent on the stability of the hairpin structure of the RNA as assessed by a comparison of transcription of the wild-type and mutated templates. The addition of Sarkosyl and transcription at an elevated temperature during the elongation reaction enhanced the production of the attenuated RNA from all templates.
Localization and Characterization of Flavivirus Envelope Glycoprotein Cross-Reactive Epitopes (2004)

ABSTRACT The flavivirus E glycoprotein, the primary antigen that induces protective immunity, is essential for membrane fusion and mediates binding to cellular receptors. Human flavivirus infections stimulate virus species-specific as well as flavivirus cross-reactive immune responses. Flavivirus cross-reactive antibodies in human sera create a serious problem for serodiagnosis, especially for secondary flavivirus infections, due to the difficulty of differentiating primary from secondary cross-reactive serum antibodies. The presence of subneutralizing levels of flavivirus cross-reactive serum antibodies may result in a dramatic increase in the severity of secondary flavivirus infections via antibody-dependent enhancement. An understanding of flavivirus E-glycoprotein cross-reactive epitopes is therefore critical for improving public health responses to these serious diseases. We identified six E-glycoprotein residues that are incorporated into three distinct flavivirus cross-reactive epitopes. Two of these epitopes which are recognized by distinct monoclonal antibodies contain overlapping continuous residues located within the highly conserved fusion peptide. The third epitope consists of discontinuous residues that are structurally related to the strictly conserved tryptophan at dengue virus serotype 2 E-glycoprotein position 231.
Lyophilized Plasma Reconstituted With Ascorbic Acid Suppresses Inflammation and Oxidative DNA Damage (2011)

Resuscitation with AA results in decreased interleukin-6 expression and oxidative DNA damage compared with CA and HCL.
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes (2005)

MicroRNAs (miRNAs) are short endogenous RNAs known to post-transcriptionally repress gene expression in animals and plants. A microarray profiling survey revealed the expression patterns of 175 human miRNAs across 24 different human organs. Our results show that proximal pairs of miRNAs are generally coexpressed. In addition, an abrupt transition in the correlation between pairs of expressed miRNAs occurs at a distance of 50 kb, implying that miRNAs separated by &lt;50 kb typically derive from a common transcript. Some microRNAs are within the introns of host genes. Intronic miRNAs are usually coordinately expressed with their host gene mRNA, implying that they also generally derive from a common transcript, and that in situ analyses of host gene expression can be used to probe the spatial and temporal localization of intronic miRNAs.
Leukemia inhibitory factor/human interleukin for DA cells: a growth factor that stimulates the in vitro development of multipotential human hematopoietic progenitors (1991)

We investigated the in vitro hematopoietic stimulatory activity of leukemia inhibitory factor/human interleukin for DA cells (LIF/HILDA) on bone marrow progenitor populations in 17 normal individuals. In serum-free cultures LIF/HILDA did not induce colony growth. In serum containing media, LIF/HILDA stimulated the growth of colony forming unit (CFU)-MIX and CFU-EO in a dose-dependent fashion and resulted in an increased CFU-MIX and burst forming unit-erythrocytes (BFU-E) colony size. Similar stimulatory effects were seen on a highly purified hematopoietic progenitor population obtained after immunomagnetic depletion of mature myeloid precursors and lymphoid cells. Addition of LIF/HILDA to cultures containing maximally stimulatory concentrations of recombinant human interleukin-3 (rhuIL3), rhuIL3 + rhuIL6, or rhu granulocyte-macrophage colony-stimulating factor (rhu GM-CSF) in serum containing media significantly increased the number of CFU-MIX and eosinophil colonies and increased size and cluster number of CFU-MIX and BFU-E. Depletion of accessory T lymphocytes or monocytes from bone marrow progenitors did not alter the response of hematopoietic precursors to LIF/HILDA. A similar increased colony growth was seen when LIF/HILDA was added to cultures of positively selected CD34/HLA- DR+ or CD34+/HLA-DR- bone marrow hematopoietic progenitor cells stimulated with maximally stimulatory concentrations of rhuIL3 + rhuIL6. LIF/HILDA is a novel cytokine capable of stimulating growth and proliferation of multi-lineage, erythroid, and eosinophil colonies in the presence of serum. LIF/HILDA exerts its activity by direct interaction with highly purified immature bone marrow progenitor cells, has an additive effect when used with other cytokines known to stimulate primitive hematopoietic precursors, and does not require accessory cells.
Joint kinematics simulation from medical imaging data (1997)

A method for joint kinematics simulation is described. Kinematics parameters are determined from the relative displacement of marker sets placed on anatomical landmarks of surface models generated from medical imaging contour data. The landmarks are identified manually on fingers in multiple positions. A mathematical algorithm was then used to ascertain the kinematics axes of motion of the fingers. Once these axes are located, they are used as the base of a real time interactive simulation of the finger. The entire simulation was accomplished in a high-resolution graphics environment. A full complement of interactive tools (virtual dials and buttons controlled via mouse) was used to enhance the user interface. The development of the system, the model and the advantages and disadvantages of the method are discussed.
Identifying the Nature of the Active Species in the Polymerization of Methacrylates:  Inhibition of Methyl Methacrylate Homopolymerizations and Reactivity Ratios for Copolymerization of Methyl Methacrylate/n-Butyl Methacrylate in Classical Anionic, Alkyllithium/Trialkylaluminum-Initiated, Group Transfer Polymerization, Atom Transfer Radical Polymerization, Catalytic Chain Transfer, and Classical Free Radical Polymerization (1997)

Reactivity ratios have been determined for the monomer pair methyl methacrylate and n-butyl methacrylate under a range of polymerization conditions. The value of using reactivity ratios as a mechanistic probe is discussed. Reactivity ratios determined where M1 = MMA and M2 = n-BMA are 1.04, 0.81, classical anionic; 1.10, 0.72 , alkyllithium/trialkylaluminum initiated; 1.76, 0.67, group transfer polymerization; 0.98, 1.26, atom transfer radical polymerization; 0.75, 0.98, catalytic chain transfer; and 0.93, 1.22, classical free radical polymerization. The data suggest ATRP and CCTP proceed via radical type propagation. Li/Al-initiated polymerization undergoes an anionic mechanism, while strong evidence is found for an associative, catalyst dependent mechanism for GTP. Galvinoxyl is demonstrated to inhibit GTP as well as free radical polymerization, and it is suggested that neither the use of inhibition nor polymer stereochemistry can be used to distinguish between anionic and radical processes.
Feasibility study on bonding quality inspection of microfluidic devices by optical coherence tomography (2011)

This paper reports the feasibility of optical coherence tomography (OCT) technology for inspection of bonding quality of microfluidic devices in manufacturing environments. A compact optical-fiber-based OCT is developed and its measurement performance is characterized. A series of microfluidic devices respectively bonded by adhesive tape, thermal method, and oxygen plasma, are inspected. The defects of geometry deformation and sealing completeness are emphasized during measurements. Based on the inspection results, some discoveries related to the production of microfluidic devices are discussed.
The medium chains of the mammalian clathrin‐associated proteins have a homolog in yeast (1991)

We have cloned and sequenced mouse brain AP47, the medium chain of the trans-Golgi network clathrin-associated protein complex AP-1. The predicted protein sequence of AP47 is closely related to rat and calf brain AP50, the corresponding medium chain of the plasma-membrane clathrin-associated protein complex AP-2. We have also identified in the yeast genome an open reading frame encoding a protein of previously unknown function. Referred to here as YAP54, its predicted protein sequence displays a striking homology to AP47. We therefore propose that Yap54 is the medium chain subunit of a putative AP-1 complex in yeast. From the analyses of the optimized sequence alignments of AP47, AP50 and Yap54p, we suggest a model for the domain organization of the medium chains.
Ultra-low latency continuous block-parallel stream windowing using FPGA on-chip memory (2017)

In this paper, we propose and demonstrate a real-time ultra-fast multi-data stream processing methodology on FPGA called “SWIM” (Stream Windowing on Interleaved Memory). The method exploits the flexible on-chip block memory fabric on existing FPGA architectures to achieve ultra-low-latency and fully pipelined continuous data flow while maintaining linear spatial locality of data for efficient data addressing and processing. The SWIM method is directly applicable to many practical applications such as real-time stencil computing, streaming image data processing, as well as closed loop-control systems that require ultra-low latency interleaved access and processing of high-speed sensor data. We demonstrate two practical cases on actual FPGA for generic 3-by-3 2-D convolution filter and image super-resolution method using pixel interleaving. Both memory usage and latency scales linearly with window height, or width of the 2-D input data set. The generic implementation of SWIM on FPGA showed impressive worst-case operation frequency of 410 MHz and uses 9.0χ and 5.6χ less Register and LUT resources respectively compared with a high-level synthesis solution.
Skinput (2011)

Skinput is a technology that appropriates the skin as an input surface by analyzing mechanical vibrations that propagate through the body. Specifically, we resolve the location of finger taps on the arm and hand using a novel sensor array, worn as an armband. This approach provides an on-body finger input system that is always available, naturally portable, and minimally invasive. When coupled with a pico-projector, a fully interactive graphical interface can be rendered directly on the body. To view video of Skinput, visit http://cacm.acm.org.
GB Virus C/Hepatitis G Virus Infection: A Favorable Prognostic Factor in Human Immunodeficiency Virus—Infected Patients? (1998)

To investigate a possible influence of GB virus C (GBV-C) in immunocompromised patients, the prevalences of GBV-C RNA and anti-E2 antibody in 197 human immunodeficiency virus (HIV)-infected patients and in 120 control blood donors were studied. GBV-C RNA was detected in 33 of 197 HIV-infected patients (16.8%) compared with 1 in 120 blood donors (0.8%) (P < .001). Previous exposure to GBV-C (anti-E2 antibody-positive) was shown in 56.8% of HIV patients and in 9% of blood donors. GBV-C viremia was not associated with hepatitis. Despite approximately equal duration of HIV infection in all subgroups, the CD4 cell counts were significantly higher in GBV-C-viremic patients (344 cells/microL) compared with exposed (259 cells/microL) and unexposed (170 cells/microL) patients (P = .017 and P < .001). Furthermore, Kaplan-Meier analysis demonstrated significantly better cumulative survival in GBV-C RNA-positive HIV-infected patients, suggesting that GBV-C might be a favorable prognostic factor in HIV disease.
Adenosine A3 receptor agonists inhibit murine macrophage tumor necrosis factor-alpha production in vitro and in vivo. (1997)

Adenosine and related analogs have been shown to regulate a variety of cell functions through different classes of adenosine receptors. Murine J774.1 macrophage cells were found to predominantly express adenosine A3 receptor RNA relative to adenosine A1 receptor or adenosine A2 receptor RNA. Adenosine receptor agonists, in a dose-dependent manner characteristic of the adenosine A3 receptor, blocked endotoxin-induction of the TNF-alpha gene and TNF-alpha protein expression in the J774.1 macrophage cell line. The adenosine A3 receptor antagonist BW-1433 dose-dependently reversed this adenosine receptor agonist inhibitory effect on TNF-alpha gene expression. Thus, the binding of adenosine receptor agonists to the adenosine A3 receptor interrupts the endotoxin CD14 receptor signal transduction pathway and blocks induction of cytokine TNF-alpha, revealing a novel cross-talk between the murine adenosine A3 receptor and the endotoxin CD14 receptor in J774.1 macrophages.
Reversible Interpenetration in a Metal–Organic Framework Triggered by Ligand Removal and Addition (2012)

Caging cages: Crystals of a metal-organic framework, MOF-123 [Zn7O2(NBD)5(DMF)2] have a three-dimensional porous structure in which DMF ligands (see picture, pink) protrude into small channels. Removal of these ligands triggers the transformation of this MOF to the doubly interpenetrating form, MOF-246 [Zn7O2(NBD)5]. Moreover, addition of DMF into MOF-246 triggers reverse transformation to give MOF-123. NBD=2-nitrobenzene-1,4-dicarboxylate.
Anthropometric manikin for acoustic research (1975)

A manikin for hearing aid and related acoustic research was designed with median human adult dimensions. Ear simulation matches the acoustic response with an auricle, an ear canal, and an eardrum that equal the median ear in dimensions, acoustic impedance and modes. Dimensions of torso and head are based on published anthropometric data, but the auricle is based on data obtained for this development. The ear canal and eardrum are adapted from the earlike coupler by Zwislocki. The ear entrance sound pressure was found to be relatively insensitive to surface or skin impedance of the head. Validating measurements show the manikin, designated KEMAR, to be like a median human in acoustic response to free fields. Subject Classification: 65.22, 65.80, 65.35,65.82.
Expression of the Proliferating Cell Nuclear Antigen in Cervical Neoplasia (1994)

The expression of the proliferating cell nuclear antigen (PCNA) was examined to determine the proliferative activity of the cells in nonneoplastic and neoplastic lesions of the uterine ectocervix. Formalin-fixed, paraffin-embedded tissue sections of uterine cervix including normal, metaplasia, condyloma, intraepithelial neoplasia and invasive squamous cell carcinoma were stained immunohistochemically using monoclonal antibody to PCNA. The percentage of PCNA-positive cells was significantly higher in premalignant and malignant lesions of the uterine cervix than in nonneoplastic lesions. Furthermore, the growth fraction of tumor cells as detected by PCNA was increased in accordance with the progression of neoplasia. The results of this study suggest that the cell proliferation index as detected immunohistochemically using PCNA may be a useful adjunct to histological diagnosis of various grades of dysplasia.
Dissection of gastric cancer heterogeneity for precision oncology (2019)

Gastric cancer (GC) remains the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. Comprehensive -omic studies have unveiled a heterogeneous GC landscape, with considerable molecular diversity both between and within tumors. Given the complex nature of GC, a long-sought goal includes effective identification of distinct patient subsets with prognostic and/or predictive outcomes to enable tailoring of specific treatments ("precision oncology"). In this review, we highlight various approaches to molecular classification in GC, covering recent genomic, transcriptomic, proteomic and epigenomic features. We pay special attention to the translational significance of classifier systems and examine potential confounding factors which deserve further investigation. In particular, we discuss recent advancements in our knowledge of intra-subtype, intra-patient and intra-tumor heterogeneity, and the pivotal role of the tumor stromal microenvironment.
Who receives contraception counseling when starting new lupus medications? The potential roles of race, ethnicity, disease activity, and quality of communication (2015)

This study demonstrates a gap in family planning counseling among women with SLE starting new medications. Future studies to address these potential areas of intervention, including education about the need for contraception through menopause, and mechanisms to engage in SDM surrounding contraception are needed to improve quality of care for women with lupus.
Poetry Out Loud: Two Perspectives, Overview (2015)

Poetry Out Loud, a national poetry recitation contest begun by the National Endowment for the Arts and the Poetry Foundation in 2006, is described from two perspectives: this short article is by the director of the Maine Arts Commission, which administers the program in Maine.
Upregulated long non-coding RNA AGAP2-AS1 represses LATS2 and KLF2 expression through interacting with EZH2 and LSD1 in non-small-cell lung cancer cells (2016)

Recently, long non-coding RNAs (lncRNAs) are identified as new crucial regulators of diverse cellular processes, including cell proliferation, differentiation and cancer cells metastasis. Accumulating evidence has revealed that aberrant lncRNA expression plays important roles in carcinogenesis and tumor progression. However, the expression pattern and biological function of lncRNAs in non-small-cell lung cancer (NSCLC) remain largely unknown. In this study, we performed comprehensive analysis of lncRNA expression in human NSCLC samples by using microarray data from Gene Expression Omnibus. After validation in a cohort of 80 pairs of NSCLC tissues, we identified a differentially expressed novel oncogenic lncRNA termed as AGAP2-AS1. The AGAP2-AS1 expression level was significantly upregulated in NSCLC tissues and negatively correlated with poor prognostic outcomes in patients. In vitro loss- and gain-of-function assays revealed that AGAP2-AS1 knockdown inhibited cell proliferation, migration and invasion, and induced cell apoptosis. In vivo assays also confirmed the ability of AGAP2-AS1 to promote tumor growth. Furthermore, mechanistic investigation showed that AGAP2-AS1 could bind with enhancer of zeste homolog 2 and lysine (K)-specific demethylase 1A, and recruit them to KLF2 and LATS2 promoter regions to repress their transcription. Taken together, our findings indicate that AGAP2-AS1 may act as an oncogene by repressing tumor-suppressor LATS2 and KLF2 transcription. By clarifying the AGAP2-AS1 mechanisms underlying NSCLC development and progression, these findings might promote the development of novel therapeutic strategies for this disease.
Rapid Control of Wound Infections by Targeted Photodynamic Therapy Monitored by In Vivo Bioluminescence Imaging¶ (2002)

The worldwide rise in antibiotic resistance necessitates the development of novel antimicrobial strategies. In this study we report on the first use of a photochemical approach to destroy bacteria infecting a wound in an animal model. Following topical application, a targeted polycationic photosensitizer conjugate between poly-L-lysine and chlorin(e6) penetrated the gram (-) outer bacterial membrane, and subsequent activation with 660 nm laser light rapidly killed Escherichia coli infecting excisional wounds in mice. To facilitate real-time monitoring of infection, we used bacteria that expressed the lux operon from Photorhabdus luminescens; these cells emitted a bioluminescent signal that allowed the infection to be rapidly quantified, using a low-light imaging system. There was a light-dose dependent loss of luminescence in the wound treated with conjugate and light, not seen in untreated wounds. Treated wounds healed as well as control wounds, showing that the photodynamic treatment did not damage the host tissue. Our study points to the possible use of this methodology in the rapid control of wounds and other localized infections.
Basic Research Needs: Catalysis for Energy (2008)

The report presents results of a workshop held August 6-8, 2007, by DOE SC Basic Energy Sciences to determine the basic research needs for catalysis research.