gebhart/patrepeval huggingface dataset:
HSF1 transcription factor concentrates in nuclear foci during heat shock: relationship with transcription sites (1997)

In this paper, we show that upon heat shock, HSF1 concentrates in the nucleus of diploid human fibroblasts in two large foci. The relative distribution of HSF1 nuclear foci and active heat shock protein (hsp) genes was investigated by combining fluorescence in situ hybridization (FISH) for the detection of hsp nuclear transcripts and immunofluorescence for the detection of HSF1. We show that the HSF1 foci are distinct from the sites of hsp70 and hsp90 genes transcription. This is the second report of ploidy-dependent foci of transcription factors that are independent of their specific transcription sites. However, the correlation between the number of HSF1 foci and the ploidy of the cells strongly supports the existence of a specific chromosomal target for HSF1 foci.
Isolation and characterization of anti-T-antigen single chain antibodies from a phage library. (2009)

T-antigen (Galbeta1-3GalNAc-Thr/Ser) also known as Thomsen-Friedenreich (TF) antigen is the core 1 structure of O-linked mucin type glycans. In normal epithelium, the disaccharide structure is masked by terminal carbohydrate moieties, but is uncovered in most primary and metastatic epithelial malignant tumors. For the purpose of establishing cancer diagnosis and therapeutics, anti-T-antigen antibodies were isolated from a phage library displaying human single chain antibodies. A strategy similar to the previously published method (Sakai et al. Biochemistry. 2007; 46:253-262) was used to screen T-antigen specific antibodies, except that a different type of glycolipid was used for panning and screening. Eleven phage clones were isolated and characterized by DNA sequencing and ELISA, which revealed 4 groups of clones with T-antigen binding activity. One single chain antibody (scFv) protein, derived from phage clone 1G11, was expressed in Escherichia coli and purified to near homogeneity by two column chromatographies. ELISA and surface plasmon resonance analyses revealed that the purified 1G11 scFv bound to the T-antigen moiety of the neoglycolipid used. This study not only demonstrated the validity of our previously introduced strategy employing the phage display technology in constructing human scFvs against various carbohydrate antigens, but also provided us with various scFv genes that can lead to future development of antibody-based therapeutics.
Efficient elimination of selectable marker genes from the plastid genome by the CRE‐lox site‐specific recombination system (2001)

Incorporation of a selectable marker gene during transformation is essential to obtain transformed plastids. However, once transformation is accomplished, having the marker gene becomes undesirable. Here we report on adapting the P1 bacteriophage CRE-lox site-specific recombination system for the elimination of marker genes from the plastid genome. The system was tested by the elimination of a negative selectable marker, codA, which is flanked by two directly oriented lox sites (>codA>). Highly efficient elimination of >codA> was triggered by introduction of a nuclear-encoded plastid-targeted CRE by Agrobacterium transformation or via pollen. Excision of >codA> in tissue culture cells was frequently accompanied by a large deletion of a plastid genome segment which includes the tRNA-ValUAC gene. However, the large deletions were absent when cre was introduced by pollination. Thus pollination is our preferred protocol for the introduction of cre. Removal of the >codA> coding region occurred at a dramatic speed, in striking contrast to the slow and gradual build-up of transgenic copies during plastid transformation. The nuclear cre gene could subsequently be removed by segregation in the seed progeny. The modified CRE-lox system described here will be a highly efficient tool to obtain marker-free transplastomic plants.
Multiple mRNAs from rat kidney and brain encode a single Na+,K+-ATPase beta subunit protein. (1987)

To determine whether multiple forms of the Na+,K+-ATPase beta subunit exist in rat kidney and brain, we constructed cDNA libraries from both tissues and isolated clones carrying inserts coding for this subunit. Characterization of these cDNAs by restriction endonuclease mapping and DNA sequencing suggests that a single form of the beta subunit protein is present in these tissues. We did, however, find that the beta subunit was encoded by multiple mRNAs which can be grouped into classes based on the lengths of their 5' and 3' untranslated regions. Size variation at the 3' end is due to the use of at least two of the five potential polyadenylation sites, whereas variation at the 5' end appears to be due to the use of different initiation sites. Northern blot analysis demonstrates the presence of multiple mRNA species which correlate with the sizes observed for the different cDNA classes and also demonstrates that the larger mRNA species are present at different levels in kidney and brain. S1 and primer extension analyses suggest that the observed tissue differences in the expression of these mRNAs are due to transcription from multiple initiation sites, whose strength is tissue-dependent. In the 3' untranslated region, comparison of the nucleotide sequence of the rat beta subunit cDNAs to those from other species reveals regions of high sequence similarity.
Biphasic Regulation of Leukocyte Superoxide Generation by Nitric Oxide and Peroxynitrite (2000)

Activation of the NADPH oxidase-derived oxidant burst of polymorphonuclear leukocytes (PMNs) is of critical importance in inflammatory disease. PMN-derived superoxide (O(2)) can be scavenged by nitric oxide (NO( small middle dot)) with the formation of peroxynitrite (ONOO(-)); however, questions remain regarding the effects and mechanisms by which NO( small middle dot) and ONOO(-) modulate the PMN oxidative burst. Therefore, we directly measured the dose-dependent effects of NO( small middle dot) and ONOO(-) on O(2) generation from human PMNs stimulated with phorbol 12-myristate 13-acetate using EPR spin trapping. Pretreatment with low physiological (microm) concentrations of NO( small middle dot) from NO( small middle dot) gas had no effect on PMN O(2) generation, whereas high levels (> or =50 microm) exerted inhibition. With ONOO(-) pretreatment, however, a biphasic modulation of O(2) generation was seen with stimulation by microm levels, but inhibition at higher levels. With the NO( small middle dot) donor NOR-1, which provides more sustained release of NO( small middle dot) persisting at the time of O(2) generation, a similar biphasic modulation of O(2) generation was seen, and this was inhibited by ONOO(-) scavengers. The enhancement of O(2) generation by low concentrations of ONOO(-) or NOR-1 was associated with activation of the ERK MAPKs and was blocked by their inhibition. Thus, low physiological levels of NO( small middle dot) present following PMN activation are converted to ONOO(-), which enhances O(2) generation through activation of the ERK MAPK pathway, whereas higher levels of NO( small middle dot) or ONOO(-) feed back and inhibit O(2) generation. This biphasic concentration-dependent regulation of the PMN oxidant burst by NO( small middle dot)-derived ONOO(-) may be of critical importance in regulating the process of inflammation.
Molecular biology of the human immunodeficiency virus type 1 (1991)

The immunodeficiency virus type 1 is a complex retrovirus. In addition to genes that specify the proteins of the virus particle and the replicative enzymes common to all retroviruses, HIV-1 specifies at least six additional proteins that regulate the virus life cycle. Two of these regulatory genes, tat and rev, specify proteins essential for replication. These proteins bind to specific sequences of newly synthesized virus RNA and profoundly affect virus protein expression. Tat and rev appear to be prototypes of novel eukaryotic regulatory proteins. These two genes may play a central role in regulating the rate of virus replication. Three other viral genes, vif, vpu, and vpr, affect the assembly and replication capacity of newly made virus particles. These genes may play a critical role in spread of the virus from tissue to tissue and from person to person. Our understanding of the contribution of each of the virus structural proteins and regulatory genes to the complex life cycle of the virus in natural infections is incomplete. However, enough insight has been gained into the structure and function of each of these components to provide a firm basis for rational antiviral drug development.
First‐in‐man allopregnanolone use in super‐refractory status epilepticus (2017)

Super-refractory status epilepticus (SRSE) is associated with high morbidity and mortality. Treatment of SRSE is complicated by progressive cortical hyperexcitability believed to result in part from synaptic GABA receptor internalization and desensitization. Allopregnanolone, a neurosteroid that positively modulates synaptic and extrasynaptic GABA<sub>A</sub> receptors, has been proposed as a novel treatment. We describe the first two patients with SRSE who were each successfully treated with a 120-h continuous infusion of allopregnanolone. Both patients recovered from prolonged SRSE with good cognitive outcomes.
Multielectron Storage and Photo‐Induced Electron Transfer in Oligonuclear Complexes Containing Ruthenium(II) Terpyridine and Ferrocene Building Blocks (2006)

Abstract The heteroleptic complex [(HOOC‐tpy)Ru(tpy‐NH 2 )](PF 6 ) 2 (tpy = 2,2′;6′,2″‐terpyridine) has been incorporated into a multicomponent system with ferrocene moieties attached on either the N‐terminal end or the C‐terminal end and on both ends of the ruthenium complex. Electrochemical studies reveal almost noninteracting subunits in the oligonuclear systems, whereas ground‐state and excited‐state optical properties are shown to strongly depend on the site of ferrocene attachment. Interpretation of the experimental results is supported by DFT calculations. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
TextTearing (2013)

Having insufficient space for making annotations is a problem that afflicts both paper and digital documents. We introduce the TextTearing technique for in situ expansion of inter-line whitespace and pair it with a lightweight interaction for margin expansion as a way to address this problem. The full system leverages the dynamism of digital documents and employs a bimanual design that combines the precision of pen with the fluidity of touch. Our evaluation found that a simpler unimanual variant of TextTearing was preferred over direct annotation and margin-only expansion. Direct annotation in naturally occurring whitespace was least preferred.
Human autoantibody recognition of DNA. (1995)

Combinatorial IgG Fab phage display libraries prepared from a systemic lupus erythematosus (SLE) donor and a healthy donor were affinity selected against human placental DNA. Human monoclonal antibody Fab fragments specific for DNA were isolated from both libraries, although Fabs of the highest affinity were isolated only from the lupus library. Generally, apparent affinities of the Fabs for human placental DNA, purified double-stranded DNA, and denatured DNA were approximately equivalent. Surface plasmon resonance indicated Fab binding constants for a double-stranded oligodeoxynucleotide of 0.2-1.3 x 10(8) M-1. The higher-affinity Fabs, as ranked by binding to human placental DNA or to the oligonucleotide probe, tested positive in the Crithidia luciliae assay commonly used in the diagnosis of SLE, and interestingly the genes encoding the heavy-chain variable regions of these antibodies displayed evidence of only minimal somatic hypermutation. The heavy chains of the SLE Fabs were characterized by a predominance of basic residues toward the N terminus of complementarity-determining region 3 (CDR3). The crucial role of heavy-chain CDR3 (HCDR3) in high-affinity DNA recognition was suggested by the creation of DNA binding in an unrelated antibody by HCDR3 transplantation from SLE antibodies. We propose that high-affinity DNA-binding antibodies can arise in SLE without extensive somatic hypermutation in the variable-region genes because of the expression of inappropriate HCDR3s.
Degradation of atrazine and related s‐triazines (1989)

Atrazine, simazine, and propazine are closely related herbicides that can be used for weed control. The degradation of s‐triazines in soil, water, and sediments has received considerable attention. In this review, the literature related to degradation of atrazine and related s‐triazines is reviewed. Particular emphasis is directed toward those substances formed along the degradative pathways and to the biodegradation aspects of mineralization. The s‐triazines are unusual in that the carbon and nitrogen ring contains no available electrons for aerobic biodegradation. The only sources of energy for aerobic biodegradation of atrazine are found on the ethyl and isopropy I groups. There is some evidence to support the concept that dealkylation of s‐triazines occurs to support the bioenergetic needs of microorganisms. Biodegradation studies with simazine or atrazine as the carbon and energy source have generally shown biodegradation of the alkyl side chains with evolution of radioactive carbon dioxide from chain‐labeled carbon. Under these conditions, ring‐labeled carbon is evolved as carbon dioxide in much smaller quantities. As a nitrogen source, microorganisms will use this s‐triazine‐ring nitrogen as well as the nitrogen in the amino groups attached to the carbons at the 4 and 6 positions of atrazine and simazine. A carbon and energy source to support microbial growth is important for biodegradation of s‐triazines for their nitrogen content.
Amidepsines, Inhibitors of Diacylglycerol Acyltransferase Produced by Humicola sp. FO-2942. I. Production, Isolation and Biological Properties. (1995)

Humicola sp. FO-2942, a soil isolate, was found to produce a series of new inhibitors of diacylglycerol acyltransferase (DGAT). Three active compounds, designated amidepsines A, B and C, were isolated from the fermentation broth of the producing strain by solvent extraction, silica gel column chromatography, ODS column chromatography and HPLC. Amidepsines inhibit DGAT activity with IC50 values of 10.2 approximately 51.6 microM in an enzyme assay system using rat liver microsomes. Amidepsines also showed specific inhibition of triacylglycerol formation in intact Raji cells, indicating that they inhibit DGAT activity in living cells.
Evaluation of an oral patient-controlled analgesia device for pain management in oncology inpatients. (2007)

An oral, patient-controlled analgesia (PCA) device uses radiofrequency identification technology to allow patients direct, controlled access to medication at the bedside. Twenty oncology inpatients participated in a pilot study to evaluate the device's design function and patient, nursing, and pharmacy satisfaction. The referring oncology physicians ordered oral pain tablets or capsules on an as-needed basis; the drugs were dispensed by the device with a specified lockout time interval and with a provision for administration of an immediate dose, if desired. In all, 95% of the patients reported that use of the device provided better pain control, since it allowed them to receive medication directly without delay. Further, 100% of the patients preferred using the device to calling a nurse for each dose of as-needed medication. All patients desired to use the device again during future hospitalizations if they required oral breakthrough pain medications. More than 80% of nurses surveyed stated that the device was reliable and easy both to program and to query about medication-dispensing data. In addition, more than 90% of nurses reported that patients' pain appeared to be better controlled when the device was used; they also indicated that the device saved them nursing time. Pharmacy staff agreed that the device's disposable medication tray was easy to fill; however, it did not save them time. The results of a Cronbach's-alpha statistic calculated for patient and nursing questionnaires showed these surveys to be reliable tools that featured consistent responses. The overall conclusion from this pilot study was that the oral PCA device was a useful, functional device that should improve pain management in selected patients in the acute care setting.
Molecular Characterization and Phylogenetic Analysis of Magnaporthae oryzae B.C. Couch Causing Blast Disease of Rice (Oryza sativa) in Kashmir (2015)

Rice blast, caused by Magnaporthe oryzae B.C. Couch, is one of the major diseases of rice resulting in heavy economic losses. The present study, carried out during 2013–14, was aimed to characterize M. oryzae, isolated from Kashmir, on morphological characters and molecular basis using sequence information of ITS region of ribosomal DNA and to study its phylogenetic relationship with other sequences retrieved from GenBank, NCBI. Morphological characters, pathogenicity test and ITS sequence analysis helped in authentic identification of the pathogen. M. oryzae colonies were dull white to grayish-black with regular margins. Conidia were pyriform, hyaline to pale olive and measured 16–23 x 4–7 μm in size. In pathogenicity assay, typical blast disease symptoms were produced. The ITS sequence of M. oryzae (Kashmir isolate) showed 99% identity (E value: 0.00) with M. oryzae sequences already available in GenBank. The sequence was submitted to NCBI (GenBank Accession No. KP310498). Phylogenetic analysis revealed that KP310498 sequence was more closely related to the sequences of Chinese and Japanese isolates of M. oryzae as compared to Indian isolates. Moreover, most of the M. oryzae sequences under study were grouped according to the host species.
Convolutional effects in transform coding with TDAC: an optimal window (1996)

Perceptual coders have proven to be highly efficient in the context of audio or video applications involving bit rate reduction. However, this efficiency is strongly limited in very low bit rate coding conditions. This paper studies the multiplicative effects of quantization in the frequency domain, when an overlapped filter bank (TDAC, time domain aliasing cancellation) is used to shape the quantization noise in a perceptually optimal way. The associated circular convolution operation generates aliased components in the time domain that are examined and subjected to minimization. A closed form expression is suggested to approximate an optimal transform window offering a desired tradeoff between the reduction of the time artifacts produced by a coarse quantization and the reduction of the stop-band leakage, relative to other transform windows commonly used.
Bees with Varroa Sensitive Hygiene preferentially remove mite infested pupae aged ≤ five days post capping (2007)

SummarySuppressed Mite Reproduction (SMR) is a trait of honey bees that provides resistance to Varroa destructor. The mechanism of resistance in SMR bees is the removal of infested pupae from capped brood, so a better name is VSH bees (acronym for Varroa Sensitive Hygiene). This study compared the removal of infested brood by VSH and control bees to determine whether VSH bees removed infested pupae of different ages at similar rates. A pair of infested combs containing all stages of pupae were transferred into each host colony (six VSH and six control colonies) for 40 hours. VSH bees removed significantly more (55%) infested cells (singly and multiply infested), than controls (13%). They removed significantly more (66%) singly infested pupae aged from one to five days post capping (cohort A) than did controls (16%). The two types did not differ in the removal of singly infested pupae aged five to 10 days post capping (cohort B) (5–22%). Many pupae were found in uncapped cells at the end of the test, and most of the uncapped pupae were infested with mites. None of the uncapped cells contained prepupae, the development stage occurring during the first three days post capping. Thus, removal of infested pupae may be triggered by stimuli in cells with pupae aged 3–5 days post capping.
The Positive and Negative Syndrome Scale (PANSS) for Schizophrenia (1987)

The variable results of positive-negative research with schizophrenics underscore the importance of well-characterized, standardized measurement techniques. We report on the development and initial standardization of the Positive and Negative Syndrome Scale (PANSS) for typological and dimensional assessment. Based on two established psychiatric rating systems, the 30-item PANSS was conceived as an operationalized, drug-sensitive instrument that provides balanced representation of positive and negative symptoms and gauges their relationship to one another and to global psychopathology. It thus constitutes four scales measuring positive and negative syndromes, their differential, and general severity of illness. Study of 101 schizophrenics found the four scales to be normally distributed and supported their reliability and stability. Positive and negative scores were inversely correlated once their common association with general psychopathology was extracted, suggesting that they represent mutually exclusive constructs. Review of five studies involving the PANSS provided evidence of its criterion-related validity with antecedent, genealogical, and concurrent measures, its predictive validity, its drug sensitivity, and its utility for both typological and dimensional assessment.
Targeted Disruption of Tyrosylprotein Sulfotransferase-2, an Enzyme That Catalyzes Post-translational Protein Tyrosine O-Sulfation, Causes Male Infertility (2006)

Tyrosine O-sulfation is a post-translational modification mediated by one of two Golgi tyrosylprotein sulfotransferases (TPST-1 and -2) expressed in all mammalian cells. Tyrosine sulfation plays an important role in the function of some known TPST substrates by enhancing protein-protein interactions. To explore the role of these enzymes in vivo and gain insight into other potential TPST substrates, TPST-2-deficient mice were generated by targeted disruption of the Tpst2 gene. Tpst2(+/-) mice appear normal and, when interbred, yield litters of normal size with a Mendelian distribution of the targeted mutation. Tpst2(-/-) mice have moderately delayed growth but appear healthy and attain normal body weight by 10 weeks of age. In contrast to Tpst1(-/-) males that have normal fertility, Tpst2(-/-) males are infertile. Tpst2(-/-) sperm are normal in number, morphology, and motility in normal media and appear to capacitate and undergo acrosomal exocytosis normally. However, they are severely defective in their motility in viscous media and in their ability to fertilize zona pellucida-intact eggs. Adhesion of Tpst2(-/-) sperm to the egg plasma membrane is reduced compared with wild type sperm, but sperm-egg fusion is similar or even increased. These data strongly suggest that tyrosine sulfation of unidentified substrate(s) play a crucial role in these processes and document for the first time the critical importance of post-translational tyrosine sulfation in male fertility.
Towards Hybrid Swimming Microrobots: Bacteria Assisted Propulsion of Polystyrene Beads (2006)

Compactness and efficiency of biomotors makes them superior to man-made actuators and a very attractive choice of actuation for micro/nanorobots. However, biomotors are difficult to work with due to complications associated with their isolation and reconstitution. To circumvent this problem, here we use flagellar motors inside the intact cell of S. marcescens bacteria. An array of bacteria is used as propeller for a 10 microm polystyrene (PS) bead. PS bead is tracked for several seconds and its displacements is compared with diffusion length of a 10 microm particle. It is shown that the bead moves with an average velocity of 17 microm/s. Orientation of adhesion of S. marcescens to polydimethylsiloxane (PDMS) chips and microscale PS fibers was also investigated. It is shown that for both substrates; only bacteria from farther behind the leading edge of the swarm adhere in end-on configuration.