gebhart/patrepeval huggingface dataset:
A Ufd2/D4Cole1e chimeric protein and overexpression of Rbp7 in the slow Wallerian degeneration ( Wld S ) mouse (2000)

Exons of three genes were identified within the 85-kilobase tandem triplication unit of the slow Wallerian degeneration mutant mouse, C57BL/Wld(S). Ubiquitin fusion degradation protein 2 (Ufd2) and a previously undescribed gene, D4Cole1e, span the proximal and distal boundaries of the repeat unit, respectively. They have the same chromosomal orientation and form a chimeric gene when brought together at the boundaries between adjacent repeat units in Wld(S). The chimeric mRNA is abundantly expressed in the nervous system and encodes an in-frame fusion protein consisting of the N-terminal 70 amino acids of Ufd2, the C-terminal 302 amino acids of D4Cole1e, and an aspartic acid formed at the junction. Antisera raised against synthetic peptides detect the expected 43-kDa protein specifically in Wld(S) brain. This expression pattern, together with the previously established role of ubiquitination in axon degeneration, makes the chimeric gene a promising candidate for Wld. The third gene altered by the triplication, Rbp7, is a novel member of the cellular retinoid-binding protein family and is highly expressed in white adipose tissue and mammary gland. The whole gene lies within the repeat unit leading to overexpression of the normal transcript in Wld(S) mice. However, it is undetectable on Northern blots of Wld(S) brain and seems unlikely to be the Wld gene. These data reveal both a candidate gene for Wld and the potential of the Wld(S) mutant for studies of ubiquitin and retinoid metabolism.
Sequence to Sequence -- Video to Text (2015)

Real-world videos often have complex dynamics, methods for generating open-domain video descriptions should be sensitive to temporal structure and allow both input (sequence of frames) and output (sequence of words) of variable length. To approach this problem we propose a novel end-to-end sequence-to-sequence model to generate captions for videos. For this we exploit recurrent neural networks, specifically LSTMs, which have demonstrated state-of-the-art performance in image caption generation. Our LSTM model is trained on video-sentence pairs and learns to associate a sequence of video frames to a sequence of words in order to generate a description of the event in the video clip. Our model naturally is able to learn the temporal structure of the sequence of frames as well as the sequence model of the generated sentences, i.e. a language model. We evaluate several variants of our model that exploit different visual features on a standard set of YouTube videos and two movie description datasets (M-VAD and MPII-MD).
Organic solvents as facilitators of polymerase chain reaction. (1991)

We have found that in a system utilizing PCR to detect transgenic mice possessing a sheep metallothionein 1a-sheep growth hormone fusion gene, amplification of a 361-base pair (bp) fragment was completely dependent on the presence of organic solvents such as dimethyl sulfoxide, glycerol or polyethylene glycol (PEG). Much lower concentrations of these solvents (ca. 2% for DMSO) were successful as PCR facilitators than have previously been reported
Multiplex Cre/lox recombination permits selective site-specific DNA targeting to both a natural and an engineered site in the yeast genome (1996)

Variant lox sites having an altered spacer region (heterospecific lox sites) are not proficient for Cre-mediated recombination with the canonical 34 bp loxP site, but can recombine with each other. By placing different heterospecific lox sites at different genomic locations, Cre can catalyze independent DNA recombination events at multiple loci in the same cell without concern that unwanted inter-locus recombination events will be generated. Such heterospecific lox sites also allow Cre to specifically target efficient integration of exogenous DNA to endogenous lox-like sequences that naturally occur in the genome. Specific targeting occurs only with a DNA vector carrying a heterospecific lox site in which the spacer region has been redesigned to match the 'spacer' region of the targeted chromosomal element. Moreover, in cells expressing a catalytically active Cre recombinase, naturally occurring lox-like sequences can exhibit almost 20% mitotic recombination. Thus, in the same cell, heterospecific lox sites can be used independently at multiple loci for integration, for deletion and for enhanced mitotic recombination, thereby increasing the repertoire of genomic manipulations catalyzed by the Cre recombinase.
Identification of distinct endoglycosidase (endo) activities in Flavobacterium meningosepticum: endo F1, endo F2, and endo F3. Endo F1 and endo H hydrolyze only high mannose and hybrid glycans (1991)

Flavobacterium meningosepticum endo-beta-acetyl-glucosaminidase F preparations have been resolved by hydrophobic interaction chromatography on TSK-butyl resin into at least three activities designated endo F1, endo F2 and endo F3 each with a unique substrate specificity. The 32-kDa endo F1 protein is the principle component representing in excess of 95% of most earlier and currently available commercial endoglycosidase preparations, the remainder being a mixture of five proteins from 32 to 43 kDa. Substrate specificity studies reveal endo F1 and endo H from Streptomyces plicatus to have nearly identical capacities to hydrolyze high-mannose oligosaccharides with a minimum Man1 alpha 3Man1 alpha 6Man1 beta 4GlcNAc1 beta 4GlcNAc structure. Although endo H will hydrolyze fucose-containing hybrid oligosaccharides at rates approaching comparable high-mannose forms, core-linked fucose reduces the hydrolysis rate of endo F1 by over 50-fold relative to high-mannose structures. Neither homogeneous endo F1 nor endo H hydrolyze complex multi-antennary glycans. The biantennary cleaving activity previously reported for endo F preparations (Tarentino, A. L., Gómez, C. M., and Plummer, T. H., Jr. (1985) Biochemistry 24, 4665-4671) is a characteristic of the contaminating endo F2 activity.
Impact of carbohydrate supplementation during endurance training on glycogen storage and performance (2009)

These results show that carbohydrate supplementation consumed during exercise training influences various muscular training adaptations, but improvements in cardiorespiratory fitness and reductions in fat mass are not affected.
KDD Cup 2001 report (2002)

This paper presents results and lessons from KDD Cup 2001. KDD Cup 2001 focused on mining biological databases. It involved three cutting-edge tasks related to drug design and genomics.
CD3+CD16+NK1.1+B220+ large granular lymphocytes arise from both alpha-beta TCR+CD4-CD8- and gamma-delta TCR+CD4-CD8- cells. (1994)

Cultivation of CD4-CD8- double negative (DN) mouse thymocytes and splenocytes with recombinant interleukin 2 (IL2) in the absence of other stimulation results in the generation of DN-CD3/TCR+CD16+NK1.1+B220+ large granular lymphocytes (LGL). Purified DN alpha-beta TCR+ thymocytes and splenocytes are CD16+IL2R alpha-IL2R beta+NK1.1+B220-CD5high. These cells are unique in that they express both CD16 and T cell receptor (TCR) which are usually mutually exclusive. In addition, they express the natural killer (NK) marker, NK1.1. Cultivation of these cells with IL2 for several days results in the generation of DN alpha-beta TCR+CD16+NK1.1+B220+CD5- LGL, suggesting that DN alpha-beta TCR+ cells in thymus and spleen are the precursors of the DN LGL reported previously. DN gamma-delta TCR+CD16-NK1.1-B220-CD5high thymocytes and splenocytes also give rise to DN gamma-delta TCR+CD16+NK1.1+B220+CD5- LGL which, as shown previously with DN alpha-beta TCR+ LGL cells, are cytotoxic against NK-sensitive YAC-1 cells. Cytotoxic activity is also induced through either CD16 or the gamma-delta TCR. DN alpha-beta TCR+ and DN gamma-delta TCR+ LGL cells are thus similar in phenotype to TCR- NK cells. DN alpha-beta TCR+ thymocytes express low levels of the gamma subunit of the high affinity immunoglobulin E receptor (Fc epsilon RI gamma) molecule, an essential component of CD16 expression. Fc epsilon RI gamma expression is greatly enhanced after cultivation with IL2, resulting in a higher surface expression of CD16. In contrast to DN alpha-beta TCR+ thymocytes, DN gamma-delta TCR+ thymocytes do not express detectable CD16 or Fc epsilon RI gamma mRNA but expression of both is induced by cultivation with IL2, leading to the expression of CD16 on the surface. Whereas CD16 molecules on both DN alpha-beta TCR+ and DN gamma-delta TCR+ LGL are associated with only Fc epsilon RI gamma homodimers, the TCR on these cells are associated with an Fc epsilon RI gamma homodimer and/or CD3 zeta-Fc epsilon RI gamma heterodimers. These results demonstrate that the Fc epsilon RI gamma subunit is a component of the TCR in a fraction of T lineage cells.
Directed Differentiation of Human Embryonic Stem Cells into the Pancreatic Endocrine Lineage (2007)

Human embryonic stem (hES) cells represent a potentially unlimited source of transplantable beta-cells for the treatment of diabetes. Here we describe a differentiation strategy that reproducibly directs HES3, an National Institutes of Health (NIH)-registered hES cell line, into cells of the pancreatic endocrine lineage. HES3 cells are removed from their feeder layer and cultured as embryoid bodies in a three-dimensional matrix in the presence of Activin A and Bmp4 to induce definitive endoderm. Next, growth factors known to promote the proliferation and differentiation of pancreatic ductal epithelial cells to glucose-sensing, insulin-secreting beta-cells are added. Pdx1 expression, which identifies pancreatic progenitors, is detected as early as day 12 of differentiation. By day 34, Pdx1+ cells comprise between 5% and 20% of the total cell population and Insulin gene expression is up-regulated, with release of C-peptide into the culture medium. Unlike another recent report of the induction of insulin+ cells in differentiated hES cell populations, we are unable to detect the expression of other pancreatic hormones in insulin+ cells. When transplanted into severe combined immunodeficiency (SCID) mice, differentiated cell populations retain their endocrine identity and synthesize insulin.
Computer-aided design of free-space opto-electronic systems (1997)

This paper presents a system capable of static and dynamic simulationsof heterogeneous opto-electronic systems. It is capable ofmodeling Gaussian optical signal propagation with mechanicaltolerancing at the system level. We present results which demonstratethe system's ability to predict the effects of various componentparameters, such as detector geometry, and system levelparameters, such as alignment tolerances, on system performance.
Practical method for full-chip optical proximity correction (1997)

We describe a method for optical proximity correction (OPC) based on the principle of aerial image matching. Three basic, sub-resolution elements are used: scattering bars, anti-scattering bars, and serifs. We examine the effects of adjusting the sizes and placements of all three elements, and report the improvements achieved, in CD uniformity, printing fidelity, resolution, and depth of focus. We describe the use of a vertex-based `geometry engine' to correct very large microprocessor-style random logic chips of up to 20 million transistors. Our experience producing over 200 full-chip i-line OPC reticles, and the extensibility of the method to deep ultraviolet wavelengths, are presented.
Metabolites of the Angiotensin II Antagonist Tasosartan:  The Importance of a Second Acidic Group (1998)

Described in this paper is the synthesis and pharmacological activity of five metabolites of the angiotensin II antagonist tasosartan (1). Of particular interest is the effect of the additional acidic group of the enol metabolite (8) on activity. As suggested by the structural-activity relationship of other angiotensin II antagonist series, a second acidic group can improve receptor binding activity but decrease in vivo activity after oral dosing. The metabolic introduction of a second acidic group in tasosartan bypasses this problem and contributes to the excellent profile of the compound. A molecular modeling study provides a rationale for the role of the enol group of 8 in AT1 receptor binding.
Macrocyclic Polyethers and Their Complexes (1972)

Abstract The most important, and almost unique, property of the macrocyclic polyethers (“crown compounds”) is their tendency to form complexes with alkali metal salts and salts with similar cations. Such complexes are held together by electrostatic attraction between the cation and the negative end of the CO dipoles. The stability of the polyether complexes depends primarily upon how well the cation fits into the polyether ring; other factors are the charge density of the cation and—in solution—the solvating power of the medium. Cyclic polyethers have been successfully employed, inter alia, in experiments with ionic compounds in organic solvents and in studies of ion transport in biological systems.
A Comprehensive Evaluation of Colonic Mucosal Isolates of Sutterella wadsworthensis from Inflammatory Bowel Disease (2011)

Inflammatory bowel disease (IBD) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. Twenty-six clinical isolates of Sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had IBD. S. wadsworthensis was initially more frequently isolated from IBD subjects, hence this comprehensive study was undertaken to elucidate its role in IBD. Utilizing these samples, a newly designed PCR was developed, to study the prevalence of this bacterium in adult patients with ulcerative colitis (UC). Sutterella wadsworthensis was detected in 83.8% of adult patients with UC as opposed to 86.1% of control subjects (p = 0.64). Selected strains from IBD cases and controls were studied to elicit morphological, proteomic, genotypic and pathogenic differences. This study reports Scanning Electron Microscopy (SEM) appearances and characteristic MALDI-TOF MS protein profiles of S. wadsworthensis for the very first time. SEM showed that the bacterium is pleomorphic, existing in predominantly two morphological forms, long rods and coccobacilli. No differences were noted in the MALDI-TOF mass spectrometry proteomic analysis. There was no distinct clustering of strains identified from cases and controls on sequence analysis. Cytokine response after monocyte challenge with strains from patients with IBD and controls did not yield any significant differences. Our studies indicate that S. wadsworthensis is unlikely to play a role in the pathogenesis of IBD. Strains from cases of IBD could not be distinguished from those identified from controls.
RIG-I ATPase Activity and Discrimination of Self-RNA versus Non-Self-RNA (2015)

The innate immune response to pathogens is based on the discrimination between self-RNA and non-self-RNA. The main determinants of this detection for RNA viruses are specific pathogen-associated molecular patterns (PAMPs) of RNA, which are detected by dedicated cytoplasmic pattern recognition receptors (PRRs). RIG-I is a PRR that specifically detects short viral dsRNAs amid a sea of cellular RNAs. Here we study the determinants of this discrimination and how RIG-I ATPase activity, the only enzymatic activity of this sensor, contributes to its activation in a manner restricted to its interaction with non-self-RNAs. We also show how the innate immune response evolves during infection via IFN expression, from a state in which discrimination of self-RNA from non-self-RNA is most important to one in which this discrimination is sacrificed for the effectiveness of the antiviral response.
58. Rett Syndrome Is Reversible and Treatable by MeCP2 Gene Therapy into the Striatum in Mice (2005)

Introduction and aims: Mutations in the methyl-CpG-binding protein 2 (MeCP2), which binds methylated DNA and regulates gene expression, cause Rett syndrome (RTT). RTT is a neurodevelopmental disorder characterized by normal early psychomotor development, followed by the loss of psychomotor skills, and by the onset of stereotyped hand movement and of gait disturbances; no effective therapy has been developed for the RTT. MeCP2 gene therapy may be a potential candidate for effective therapy for the RTT, however, due to no experimental trial, the potential effectiveness of conducting MeCP2 gene therapy is unknown from the following biological viewpoints. The expression of MeCP2 begins during embryonic development and the expression levels of MeCP2 are high in all neurons in normal humans and mice after birth, whereas the neurological functions that MeCP2 regulates remain largely unknown. Thus, it is not possible to hypothesize whether the expression of an intact MeCP2 gene can, following the onset, modulate pre-established neurological symptoms. An additional obstacle is the fact that all of the current vectors allow only local gene delivery, although MeCP2 is expressed in all neurons in normal humans. Here we show that local delivery of the MeCP2 gene into the striatum of MeCP2-deleted mice remarkably improved the pre-established symptoms of impaired locomotion and self-injury.
Renovascular Hypertension From Renal Artery Compression by Congenital Bands (1976)

Renal artery compression by fibromuscular bands containing sympathetic nerves and ganglia was encountered in 3 of 75 patients with renovascular hypertension. The hypertension was successfully managed by resection of the bands. The absence of mortality and morbidity dictates that the "stenotic" area of the renal artery be explored, especially in children and adults with minimal angiographic evidence of visceral atherosclerosis, before proceeding with a bypass graft to the renal artery.
Huntingtin toxicity in yeast model depends on polyglutamine aggregation mediated by a prion-like protein Rnq1 (2002)

The cause of Huntington's disease is expansion of polyglutamine (polyQ) domain in huntingtin, which makes this protein both neurotoxic and aggregation prone. Here we developed the first yeast model, which establishes a direct link between aggregation of expanded polyQ domain and its cytotoxicity. Our data indicated that deficiencies in molecular chaperones Sis1 and Hsp104 inhibited seeding of polyQ aggregates, whereas ssa1, ssa2, and ydj1-151 mutations inhibited expansion of aggregates. The latter three mutants strongly suppressed the polyQ toxicity. Spontaneous mutants with suppressed aggregation appeared with high frequency, and in all of them the toxicity was relieved. Aggregation defects in these mutants and in sis1-85 were not complemented in the cross to the hsp104 mutant, demonstrating an unusual type of inheritance. Since Hsp104 is required for prion maintenance in yeast, this suggested a role for prions in polyQ aggregation and toxicity. We screened a set of deletions of nonessential genes coding for known prions and related proteins and found that deletion of the RNQ1 gene specifically suppressed aggregation and toxicity of polyQ. Curing of the prion form of Rnq1 from wild-type cells dramatically suppressed both aggregation and toxicity of polyQ. We concluded that aggregation of polyQ is critical for its toxicity and that Rnq1 in its prion conformation plays an essential role in polyQ aggregation leading to the toxicity.
Intramammary Application of Ozone Therapy to Acute Clinical Mastitis in Dairy Cows. (2000)

The infusion of ozone into the inflamed quarter of cows with clinical mastitis was performed and the efficacy of ozone therapy was evaluated. Ozone was infused into the inflamed quarter via a teat canal using ozone gas generating equipment. Nineteen Holstein cows with acute clinical mastitis were divided into two groups: 15 cows treated with ozone therapy, and 4 cows treated with antibiotic therapy. Systemic and local clinical signs, California Mastitis Test scores, the mastitis causing pathogens, electronic conductivity of milk, and somatic cell counts in milk from ozone- and antibiotic-treated quarters, were compared between the groups. Sixty percent (9/15) of cows with acute clinical mastitis treated with ozone therapy, did not require any antibiotics for recovery. This newly developed ozone therapy method was proven to be effective, safe, and cost effective, and carries no risk of drug residues in milk.
Integration of hot water extraction in biomass based CHP plants : possibilities for green chemicals and increased electricity production (2010)

The main objective of this thesis was to investigate the possibility to increase the steam temperature in the superheater in biomass (hard wood) fired CHP plants by the integration of a hemicellulose hot-water extraction process. This was motivated due to the cleaner fuel (extracted wood chips) obtained after the extraction process. One important result from the chemical analysis of the extracted wood-chips was the removal of a large share of the inorganic constituents, except Chlorine and Sulphur, from the lignocellulosic biomass. Some of those inorganic constituents (alkalis) are believed to be responsible for the fireside heat exchanger and boiler walls corrosion problems during combustion. A large portion of the current work aimed to investigate the possibility to increase the superheated steam temperature in biomass fired boilers. Thermodynamic equilibrium calculations were performed for the extracted as well as for the original birch wood chips combustion using FactSage 6.0. The results showed significant differences in equilibrium concentrations between the fuels, which could be relevant initial step towards increased temperature operation in biomass fired boilers. Converting those results into possible operational steam temperature increment is something that needs further research. A techno-economic analysis was performed for a new integrated process that produces ethanol and acetic acid from hardwood (Birch) in addition to electricity and heat. The process involves the extraction of hemicellulose content of hardwood using water at a temperature of 160 - 180℃ and a pressure of 7 bars. The extraction process is integrated into a biomass fired CHP plant. The unit operations considered in this work include a boiler/turbo-generator which operate on Rankine cycle, extraction and hydrolysis pressurized vessel, liquid-liquid separation process (for separation of acetic acid and fermentable sugars), and fermentation and ethanol up-grading processes. The hot-water extraction process at this stage is assumed to operate batch wise and heat was supplied from boiler exhaust gases. Results show low ethanol yield rate from hardwood through the hot-water extraction pathway, 0.0356 kg/ kg drywood, as compared to the current SHF (Separate Hydrolysis and Fermentation) technologies from hardwood conversion rate. This is due to the fact that hot-water extraction process dissolves the hemicellulose portion of the lignocellulosic biomass and the cellulose remains intact in the extracted chips. In addition to ethanol the process yields 0.0276 kg/kg drywood of acetic acid. Under the assumed economic conditions, ethanol can be produced to a cost in the range of SEK 3.4 to SEK 11 per litre depending on the plant size and annual operational hours. Electricity can be generated to a cost in the range of SEK 450, for the case with 100MW plant size and 8400 annual operational hours, to SEK 1120 per MWhel, for the case with 10MW plant size and 2000 operational hours per year.