gebhart/patrepeval huggingface dataset:
Distinct Patterns of DNA Damage Response and Apoptosis Correlate with Jak/Stat and PI3Kinase Response Profiles in Human Acute Myelogenous Leukemia (2010)

Characterizing and tracking changes in intracellular pathway profiles in cell subpopulations both at baseline and under therapeutic pressure will likely have important clinical applications, potentially informing the selection of beneficial targeted agents, used either alone or in combination with chemotherapy.
Stimulation of human B cells specific for Candida albicans for monoclonal antibody production (1992)

The stimulation and immortalisation of human peripheral blood B lymphocytes specific for Candida albicans antigen were investigated. An in vitro immunisation system was employed which involved pretreatment of mononuclear cells with l-leucyl l-leucine methyl ester which removes the suppressive effects of CD8 + T cells, NK cells and monocytes. The remaining cells, CD4 + T cells, B cells and dendritic cells, were cultured with antigen and a mixture of cytokines. A mixture of IL-2, −4 and −6 was found to be optimal for antibody production as determined by an Elispot assay. Transformation of the activated B cells by Epstein Barr virus was found to be optimal after 2 days and lines secreting anti-Candida antibodies were established. These lines could form the basis for specific monoclonal antibody production by generating hybridomas, or by a newly described technique whereby cDNA encoding antibody Fab regions is transferred into phage display libraries. The overall strategy might be generally applicable for the generation of human monoclonal antibodies to infectious agents.
Functional annotation of mammalian genomic DNA sequence by chemical mutagenesis: A fine-structure genetic mutation map of a 1- to 2-cM segment of mouse chromosome 7 corresponding to human chromosome 11p14-p15 (2002)

Eleven independent, recessive, N-ethyl-N-nitrosourea-induced mutations that map to a approximately 1- to 2-cM region of mouse chromosome (Chr) 7 homologous to human Chr 11p14-p15 were recovered from a screen of 1,218 gametes. These mutations were initially identified in a hemizygous state opposite a large p-locus deletion and subsequently were mapped to finer genomic intervals by crosses to a panel of smaller p deletions. The 11 mutations also were classified into seven complementation groups by pairwise crosses. Four complementation groups were defined by seven prenatally lethal mutations, including a group (l7R3) comprised of two alleles of obvious differing severity. Two allelic mutations (at the psrt locus) result in a severe seizure and runting syndrome, but one mutation (at the fit2 locus) results in a more benign runting phenotype. This experiment has added seven loci, defined by phenotypes of presumed point mutations, to the genetic map of a small (1-2 cM) region of mouse Chr 7 and will facilitate the task of functional annotation of DNA sequence and transcription maps both in the mouse and the corresponding human 11p14-p15 homology region.
Naturally Presented Peptides on Major Histocompatibility Complex I and II Molecules Eluted from Central Nervous System of Multiple Sclerosis Patients (2009)

Tandem mass spectrometry was used to identify naturally processed peptides bound to major histocompatibility complex (MHC) I and MHC II molecules in central nervous system (CNS) of eight patients with multiple sclerosis (MS). MHC molecules were purified from autopsy CNS material by immunoaffinity chromatography with monoclonal antibody directed against HLA-A, -B, -C, and -DR. Subsequently peptides were separated by reversed-phase HPLC and analyzed by mass spectrometry. Database searches revealed 118 amino acid sequences from self-proteins eluted from MHC I molecules and 191 from MHC II molecules, corresponding to 174 identified source proteins. These sequences define previously known and potentially novel autoantigens in MS possibly involved in disease induction and antigen spreading. Taken together, we have initiated the characterization of the CNS-expressed MHC ligandome in CNS diseases and were able to demonstrate the presentation of naturally processed myelin basic protein peptides in the brain of MS patients.
Substitutional or Interstitial Site-Selective Nitrogen Doping in TiO2 Nanostructures (2015)

Herein, we report a colloidal wet-chemical approach enabling control on dopant concentration and location in a nanocrystal host lattice. Growth-doping and nucleation-doping, driven by primary and tertiary amines, respectively, were identified as predominant doping mechanisms responsible for the introduction of nitrogen impurities in interstitial and substitutional sites in highly branched rutile TiO2 nanostructures. High-resolution X-ray photoelectron spectroscopy was used to distinguish the two nitrogen occupational lattice sites and, in combination with UV–vis absorption spectroscopy, to investigate the impact of the nitrogen impurities on the optoelectronic properties. The implementation of the nitrogen-doped titania nanostructures in photoelectrodes for water oxidation suggests that these atomically defined building blocks can function as a platform to investigate the impact of the nitrogen occupational sites on the photocatalytic properties. By deliberately choosing precursors and reaction conditions, instead of relying on the most common high temperature annealing of preformed metal oxide in ammonia, we emphasize the importance of understanding the chemistry behind doping to achieve an unprecedented level of control on effective dopant introduction and, therefore, property tunability.
Understanding Interactive Legends: a Comparative Evaluation with Standard Widgets (2010)

Abstract Interactive information visualization systems rely on widgets to allow users to interact with the data and modify the representation. We define interactive legends as a class of controls combining the visual representation of static legends and interaction mechanisms of widgets. As interactive legends start to appear in popular websites, we categorize their designs for common data types and evaluate their effectiveness compare to standard widgets. Results suggest that 1) interactive legends can lead to faster perception of the mapping between data values and visual encodings and 2) interaction time is affected differently depending on the data type. Additionally, our study indicates superiority both in terms of perception and interaction of ordinal controls over numerical ones. Numerical techniques are mostly used in today's systems. By providing solutions to allowing users to modify ranges interactively, we believe that interactive legends make it possible to increase the use of ordinal techniques for visual exploration.
The influence of sleep position and obesity on sleep apnea (2000)

The influence of sleep position and the degree of obesity were examined in 257 subjects with sleep apnea. Subjects were divided into three groups according to obesity: normal weight (body mass index (BMI) under 24.0 kg/m2), mild obese (BMI 24.0-26.4 kg/m2) and obese group (BMI 26.4 kg/m2 and heavier). The apnea + hypopnea index (AHI), the intraesophageal pressure and the lowest oxygen saturation became significantly worse according to the degree of obesity. The subjects were also divided into two groups according to the reduction in the AHI by lateral position: good responders showed 50% or more reduction of AHI in lateral position and poor responders indicated less than 50% reduction. The percentage of good responders to sleep position change was 90.9% in normal weight group, 74.0% in mild obese group and 57.4% in the obese group. The ratio of the subjects who had indicated two or more obstructive sites in normal weight group was 36.0% in good responders and 40.0% in poor responders. The ratio in the mild obese group was 51.8% in good responders and 66.7% in poor responders. In the obese group, the ratio was 59.4% in good responders and 78.9% in poor responders.
Osteoclastic inhibition: an action of nitric oxide not mediated by cyclic GMP. (1991)

The osteoclast is unique in its ability to resorb bone, and excessive osteoclastic activity has been implicated in osteoporosis, Paget disease of bone, rheumatoid arthritis, and the growth of metastases in bone. The activity of this cell is controlled by the main circulating inhibitor, calcitonin, in association with locally produced modulators. We show that nitric oxide (NO) may be an important member of the latter group. NO is produced by the vascular endothelium and nervous system and is involved in both neurotransmission and the regulation of blood pressure. However, our results show that the autocoid is also a potent inhibitor of osteoclast function. NO (30 microM) produced a decrease to approximately 50% of the original osteoclast spread area. Similar effects were also produced by 3-morpholinosydnonimine or sodium nitroprusside, reagents that spontaneously release NO. These shape changes were associated with a reduction of bone resorption after a 24-hr incubation of isolated osteoclasts on devitalized bone slices. NO is thought to act by stimulating guanylate cyclase, with a consequent increase in cyclic GMP, but a different mode of action is likely in the osteoclast since dibutyryl or 8-bromo cyclic GMP have no effect. It should be noted that calcitonin can produce similar changes in shape and activity but is associated with an increase in osteoclast intracellular calcium and cessation of membrane movement; neither of these is produced by NO, suggesting that its mode of action is different. The abundance of NO-producing endothelial cells in bone marrow and their proximity to osteoclasts suggests that marrow endothelial cells may play a physiological role in the regulation of osteoclastic activity.
A serine/arginine-rich nuclear matrix cyclophilin interacts with the C- terminal domain of RNA polymerase II (1997)

The largest subunit of RNA polymerase II shows a striking difference in the degree of phosphorylation, depending on its functional state: initiating and elongating polymerases are unphosphorylated and highly phosphorylated respectively. Phosphorylation mostly occurs at the C-terminal domain (CTD), which consists of a repetitive heptapeptide structure. Using the yeast two-hybrid system, we have selected for mammalian proteins that interact with the phosphorylated CTD of mammalian RNA polymerase II. A prominent isolate, designated SRcyp/CASP10, specifically interacts with the CTD not only in vivo but also in vitro . It contains a serine/arginine-rich (SR) domain, similar to that found in the SR protein family of pre-mRNA splicing factors, which is required for interaction with the CTD. Most remarkably, the N-terminal region of SRcyp includes a peptidyl-prolyl cis - trans isomerase domain characteristic of immunophilins/cyclophilins (Cyp), a protein family implicated in protein folding, assembly and transport. SRcyp is a nuclear protein with a characteristic distribution in large irregularly shaped nuclear speckles and co-localizes perfectly with the SR domain-containing splicing factor SC35. Recent independent investigations have provided complementary data, such as an association of the phosphorylated form of RNA polymerase II with the nuclear speckles, impaired splicing in a CTD deletion background and inhibition of in vitro splicing by CTD peptides. Taken together, these data indicate that factors directly or indirectly involved in splicing are associated with the elongating RNA polymerases, from where they might translocate to the nascent transcripts to ensure efficient splicing, concomitant with transcription.
Mutational analysis of cell cycle arrest, nuclear localization and virion packaging of human immunodeficiency virus type 1 Vpr (1995)

Human immunodeficiency virus type 1 Vpr is a virion-associated, regulatory protein that is required for efficient viral replication in monocytes/macrophages. The protein is believed to act in conjunction with the Gag matrix protein to allow import of the viral preintegration complex in nondividing cells. In cells, Vpr localizes to the nucleus. Recently, we showed that Vpr prevents the activation of p34cdc2-cyclin B. This results in arrest of Vpr-expressing cells in the G2/M phase of the cell cycle. Here, we use a panel of expression vectors encoding Vpr molecules mutated in the amino-terminal alpha-helical region, the central hydrophobic region, or the carboxy-terminal basic region to define the functional domains of the protein. The results showed cell cycle arrest was largely controlled by the carboxy-terminal basic domain of the protein. In contrast, the amino-terminal alpha-helical region of Vpr was required for nuclear localization and packaging into virions. The carboxy terminus appeared to be unnecessary for nuclear localization. In the alpha-helical region, mutation of Ala-30 to Pro resulted in a protein that localized to the cytoplasm. Surprisingly, fusion of Vpr to luciferase resulted in a molecule that failed to localize to the nucleus. In addition, we show that simian immunodeficiency virus Vpr, but not Vpx, induces G2 arrest. We speculate that Vpr has two sites for interaction with cellular factors: one in the alpha-helical region that specifies nuclear localization and one in the carboxy-terminal domain that is required for Cdc2 inhibition.
Serology assays to manage COVID-19 (2020)

Measurement of antibodies to SARS-CoV-2 will improve disease management if used correctly
EXTRACTION OF OLIGOSACCHARIDES DURING COOKING OF WHOLE SOYBEANS (1976)

ABSTRACT Raffinose and stachyose present in soybeans have been reported to cause flatulence. The objective of this work was to study the aqueous extraction of whole soybeans during water cooking to determine optimum conditions for maximum removal of oligosaccharides with minimum loss of protein. Chief variables were bean to water ratio (1:3, 1:5, 1:7.5 and 1:10) and pH. Residual oligosaccharides in the soybeans were determined by silylation followed by GLC analysis. During 20 min boiling in water, a 1:10 ratio resulted in 33% oligosaccharide extraction (g per 100g original oligosaccharide) with 1% protein loss (g per 100g original protein) while a 1:3 ratio gave only 7.7% oligosaccharide removal with 0.9% protein loss. When the time was extended to 60 min, a 1:10 ratio resulted in 59% extraction with 2.6% protein loss and 12% total solids loss (g per 100g original soybean solids). With the latter treatment, sucrose fell from 6.5 to 3.0% dry basis and fructose fell from 1.6% to 1.0%. Addition of 0.5% NaHCO 3 to the tap water (initial pH 8.1) increased ohgosaccharide removal but trebled protein loss to 6.8% while addition of HCI to initial pH 4.3 gave about the same protein loss and oligosaccharide removal as tap water.
Evidence for enhanced rates of complement activation in serum from patients with newly diagnosed insulin-dependent diabetes mellitus exposed to rat islet cells and complement-dependent induction of islet cell apoptosis (1999)

In this paper we report the concentration of terminal complement complexes (TCCs, SC5b-9, an index of complement activation) in newly diagnosed insulin-dependent diabetes mellitus (IDDM) patient serum and normal human serum. In the nine patients studied, levels of serum soluble TCCs were approximately 1.6-fold higher than in sera obtained from normal control individuals. On incubation of rat islet cells with diluted serum (10%, v/v, concentration), complement activation was increased at a significantly faster rate and the total TCC concentration was significantly higher in culture medium containing IDDM patient serum than in medium containing control serum. The concentration of anti-(glutamic acid decarboxylase) autoantibodies in newly diagnosed IDDM patient serum was on average 60-fold higher than in normal human control serum. IDDM patient serum (10%, v/v) induced apoptosis in islet cells, as determined by islet cell density changes and DNA fragmentation patterns. However, serum from IDDM patients was not able to induce apoptosis of the cells when complement components (C1q and C3) or antibodies were depleted. In addition, glutamine and the potent antioxidant 1-pyrrolidinecarbodithioic acid partially reversed cell death induced by IDDM patient serum in a concentration-dependent manner. The ATP concentration in islet cells incubated for 24 h in the presence of diluted IDDM patient serum was reduced to 4.4% of that observed in islet cells incubated in fetal calf serum or 7.3% of that observed in islet cells incubated in normal human serum. On the basis of these observations, we suggest that the pathway of IDDM patient serum-induced islet cell apoptosis may involve antibody-dependent complement activation, free radical generation and a precipitous fall in ATP levels.
Human Bocavirus: Prevalence and Clinical Spectrum at a Children’s Hospital (2006)

HBoV DNA is commonly present in children with upper and lower respiratory tract infections. The presence of a pertussis-like cough and diarrhea in association with HBoV infection merits further investigation.
The Effects of Obesity on Orthopaedic Foot and Ankle Pathology (2007)

Tendinitis, plantar fasciitis, and osteoarthritis usually are secondary to overuse and increased stress on the soft tissues and joints, which may be directly related to increased weight on these structures.
Transcriptional repressor ZF5 identifies a new conserved domain in zina finger proteins (1993)

We have cloned a cDNA encoding a new murine C2H2 zinc finger protein, ZF5. The 51.3 kD protein contains five GL1-Kruppel type zinc fingers at the C-terminus. At its N-terminus, ZF5 has a 41 amino acid region which was found to be homologous to the N-termini of several other zinc finger proteins. This region defines a new motif within zinc finger proteins which we have named the Zinc finger N-terminal (ZiN) domain. ZF5 binds to two sites in the c-myc promoter and to the -50 bp site of the herpes simplex thymidine kinase promoter. ZF5 is a transcriptional repressor and its repression domain is located N-terminal to the zinc finger domains. A single 4 kb ZF5 mRNA is expressed widely.
Identification of Borrelia burgdorferi and B. hermsii using DNA hybridization probes (1989)

Fragments of plasmid DNA from Borrelia burgdorferi and B. hermsii were cloned and tested for specificity as hybridization probes to identify these two species of pathogenic spirochetes. Three fragments from the 49-kilobase-pair linear plasmid of B. burgdorferi were tested: a 500-base-pair (bp) HindIII fragment (probe 49A), a 445-bp PstI-HindIII fragment (probe 3G), and a 320-bp HindIII fragment (probe 16H). When hybridized to purified DNA or whole spirochetes, all of the probes distinguished B. burgdorferi from the other species examined, including B. hermsii, B. parkeri, B. turicatae, B. coriaceae, B. crocidurae, and B. anserina. Probe 49A was the most useful, however, hybridizing with all strains of B. burgdorferi originating from both North America and Europe while not cross-hybridizing with B. hermsii. A 790-bp HindIII fragment of B. hermsii DNA hybridized with DNA and whole spirochetes of this species and also with B. parkeri, confirming the close relatedness of these two species. These probes provide a new method of identifying these Borrelia species once the organisms have been grown in culture.
Lineage tracing demonstrates the venous origin of the mammalian lymphatic vasculature (2007)

The origin of the mammalian lymphatic vasculature has been debated for more than 100 years. Whether lymphatic endothelial cells have a single or dual, venous or mesenchymal origin remains controversial. To resolve this debate, we performed Cre/loxP-based lineage-tracing studies using mouse strains expressing Cre recombinase under the control of the Tie2, Runx1, or Prox1 promoter elements. These studies, together with the analysis of Runx1-mutant embryos lacking definitive hematopoiesis, conclusively determined that from venous-derived lymph sacs, lymphatic endothelial cells sprouted, proliferated, and migrated to give rise to the entire lymphatic vasculature, and that hematopoietic cells did not contribute to the developing lymph sacs. We conclude that the mammalian lymphatic system has a solely venous origin.
Temporal regularized matrix factorization for high-dimensional time series prediction (2016)

Time series prediction problems are becoming increasingly high-dimensional in modern applications, such as climatology and demand forecasting. For example, in the latter problem, the number of items for which demand needs to be forecast might be as large as 50,000. In addition, the data is generally noisy and full of missing values. Thus, modern applications require methods that are highly scalable, and can deal with noisy data in terms of corruptions or missing values. However, classical time series methods usually fall short of handling these issues. In this paper, we present a temporal regularized matrix factorization (TRMF) framework which supports data-driven temporal learning and forecasting. We develop novel regularization schemes and use scalable matrix factorization methods that are eminently suited for high-dimensional time series data that has many missing values. Our proposed TRMF is highly general, and subsumes many existing approaches for time series analysis. We make interesting connections to graph regularization methods in the context of learning the dependencies in an autoregressive framework. Experimental results show the superiority of TRMF in terms of scalability and prediction quality. In particular, TRMF is two orders of magnitude faster than other methods on a problem of dimension 50,000, and generates better forecasts on real-world datasets such as Wal-mart E-commerce datasets.
Cholesterol derivative of a new triantennary cluster galactoside directs low- and high-density lipoproteins to the parenchymal liver cell (1994)

We have developed a new triantennary galactoside, in which the terminal galactose moieties are connected to the branching point of the cluster galactoside via a 20 A (2 nm) spacer [TG(20A)]. In vitro binding studies have demonstrated that introduction of a 20 A spacer resulted in avid and specific binding of the triantennary galactoside to the asialoglycoprotein receptor on the parenchymal liver cell. Derivatization of this galactoside with a cholesterol moiety afforded a compound [TG(20A)C] that lowered the serum cholesterol concentration when injected into rats. In the present study we have evaluated the direct effect of TG(20A)C on the in vivo fate of high-density lipoprotein (HDL) and low-density lipoprotein (LDL). A direct association of TG(20A)C with HDL and LDL was observed on mixing these components. Incorporation of TG(20A)C into 125I-HDL and 125I-LDL significantly accelerated the serum decay and concomitantly stimulated the hepatic uptake of these lipoproteins in rats. The liver uptake of TG(20A)C-loaded 125I-HDL or 125I-LDL could be inhibited by 81% and 82% respectively by preinjection of 150 mg of N-acetylgalactosamine, indicating that the enhanced liver uptake proceeded via galactose-specific receptors. More than 96% of the hepatic uptake of TG(20A)C-loaded 125I-HDL could be attributed to the parenchymal cell. Surprisingly, the parenchymal cell also accounted for 93% of the liver association of TG(20A)C-loaded 125I-LDL, suggesting that TG(20A)C stimulates the uptake and processing of both lipoproteins by the asialoglycoprotein receptor on the parenchymal liver cell. This contrasts with earlier data indicating that a triantennary cluster galactoside provided with a 4 A spacer between the terminal galactose moieties and the branching point of the dendrite stimulated hepatic uptake of LDL via the Kupffer cells. The parenchymal cell is the only liver cell type that is capable of irreversibly removing cholesterol from the body in the form of bile acids. The above results imply that administration of TG(20A)C not only facilitates the hepatic uptake of lipoprotein-derived cholesterol (esters) but also their elimination from the body. In addition, it might be possible to utilize TG(20A)C as a targeting device to selectively deliver large drug carriers and possibly genes to the parenchymal liver cell.