gebhart/patrepeval huggingface dataset:
Crystal structure of a CRISPR RNA–guided surveillance complex bound to a ssDNA target (2014)

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.
Genetic systems development in the clostridia (1995)

This review describes recent developments in the genetic manipulation of the solventogenic clostridia, Clostridium acetobutylicum and C. beijerinckii. It is to be noted that our laboratory stock of C. acetobutylicum ATCC 824, which was obtained from the American Type Culture Collection, has recently been re-identified as C. beijerinckii NCIMB 8052 based on DNA similarity studies using the S1 nuclease method (personal communication, Dr. Jiann-Shin Chen, Virginia Polytechnic Institute and State University). Reference to our laboratory 824 culture has been changed to C. beijerinckii NCIMB 8052 throughout this paper in order to be consistent with this finding. The focus of this review specifically involves the characterization of an M13-like genetic system for the clostridia based on the pCAK1 phagemid, as well as preliminary work on development of a plasmid-based vector based on the indigenous pDM11 plasmid recovered from C. acetobutylicum NCIB 6443. The construction of a C. beijerinckii strain with amplified endoglucanase activity was achieved by inserting the engB gene from C. cellulovorans into C. beijerinckii. The successful expression of a heterologous engB gene from C. cellulovorans in C. beijerinckii NCIMB 8052 has important industrial significance for the eventual utilization of cellulose by this acetone-butanol-ethanol fermentation microorganism.
The Prevention of Radiocontrast-Agent–Induced Nephropathy by Hemofiltration (2003)

In patients with chronic renal failure who are undergoing percutaneous coronary interventions, periprocedural hemofiltration given in an ICU setting appears to be effective in preventing the deterioration of renal function due to contrast-agent-induced nephropathy and is associated with improved in-hospital and long-term outcomes.
Targeting the B cell receptor pathway in chronic lymphocytic leukemia (2012)

The B cell receptor (BCR) pathway plays a crucial role in the survival, proliferation and trafficking of chronic lymphocytic leukemia (CLL) cells. Inhibitors of the key kinases in this pathway, including spleen tyrosine kinase (SYK), mammalian target of rapamycin (mTOR), phosphoinositide 3'-kinase (PI3K) and Bruton's tyrosine kinase (BTK), have been found in preclinical models to decrease CLL cell viability both directly and indirectly through modulation of the microenvironment. Recently, oral agents targeting each of these kinases have been explored in early phase clinical trials in patients with CLL. BCR pathway antagonists appear to be highly active in relapsed/refractory CLL, independent of high-risk disease markers such as del(17p). These agents have shown a unique pattern of inducing early transient lymphocytosis, which typically is associated with nodal response. Here, we review the biology of the BCR, the kinases within this pathway and their interaction with the CLL microenvironment. We also discuss data from recent and ongoing clinical trials of BCR antagonists. We address the development of potential biomarkers for response to these agents such as ZAP-70, IGHV status and CCL3, and discuss where these exciting new drugs may fit in the evolving landscape of CLL therapy.
Rheological Properties of Surfactant-Based and Polymeric Nano-Fluids (2013)

Abstract Nanotechnology is well established in several industries. However, the emergence of its application is recent in the oil and gas industry; a fact corroborated by the current surge of publication in literature. Interestingly, advancement in research has shown that nanotechnology can improve the rheological properties of surfactant-based fluids (SBF) and polymeric fluids. To date, this application focuses more on polymeric fluids than on SBF. Furthermore, a few or none of the studies address the detrimental effect of nanotechnology on rheological properties of these fluids once certain limits are exceeded. Likewise, little or no information is available regarding the application of nanotechnology in SBF-polymeric fluid blends. This paper presents an experimental investigation of nanotechnology on the rheological properties of SBF, polymeric fluids, and SBF-polymeric fluid blends. The surfactant-based and polymeric fluids are composed of 5% SBF in 4% KCl and 33 lb/Mgal guar in 4% KCl respectively. Blend A was prepared by adding 75% vol. of surfactant-based fluid to 25% vol. of polymeric fluid; while Blend B resulted from the addition of 25 and 75% vol. of these fluids. The 20 nm silica nanoparticles were added to achieve three nano-fluid concentrations (0.058%, 0.24%, and 0.4% wt.) for each clean fluid. Rheological data were gathered by conducting viscometry and frequency sweep tests using the Bohlin CS-50 rheometer within a temperature range of 75 to 175 °F. The results indicate that 20 nm silica nanoparticles are beneficial in terms of enhancing rheological properties in surfactant-based and polymeric nano-fluids up to particle concentration of 0.24% and 0.4% respectively. Blend A nano-fluids show similar results at 0.058%, and only at 0.4% at high shear rates. Similarly, Blend B displayed favorable results up to 0.24% and at high temperature applications only (125 to 175 °F). Finally, relative viscosity correlations are developed for predicting viscosity of nano-suspensions. The application of nanotechnology on the rheological properties of SBF, polymeric fluids, and SBF-polymeric fluid blends delivers on great benefits, if nanoparticle concentrations are carefully selected. These nano-fluids will be applicable for oilfield operations such as hydraulic fracturing.
Phosphorothioate-Capped Antisense Oligonucleotides to Ras GAP Inhibit Cell Proliferation and Trigger Apoptosis but Fail to Downregulate GAP Gene Expression (1996)

We have studied the effects of an antisense oligonucleotide to Ras GAP in leukaemia cell lines. When terminal phosphorothioate linkages were introduced into this oligonucleotide, it caused major growth inhibition and apoptosis in the chronic myeloid leukaemia (CML) cell line K562, but had little effect on the promyelocytic leukaemia cell line HL60. Neither the expression of Ras GAP mRNA nor p120 GAP protein was downregulated by the antisense oligonucleotide, suggesting a non-antisense mechanism for growth inhibition. The antisense oligonucleotide contained GGC triplets which have previously been reported to inhibit the activity of p210bcr-abl both in vitro and in vivo. However, cellular phosphotyrosine levels were found to be unaffected, suggesting that the activity of p210bcr-abl was normal and that the antisense oligonucleotide may be interacting aptamerically with a different cellular protein. Since K562 is very resistant to apoptotic cell death, the identity of the putative target molecule would be of considerable interest.
Lipopolysaccharide augments HLA-A,B,C molecule expression but inhibits interferon-gamma-induced HLA-DR molecule expression on cultured human endothelial cells. (1991)

The effect of bacterial lipopolysaccharide (LPS) on the expression of class I and II major histocompatibility complex (MHC) molecules on the surface of cultured human umbilical vein endothelial cells (HUVEC) was determined by indirect immunofluorescent staining followed by flow cytometric analysis. LPS at concentrations higher than 0.01 micrograms/ml augmented class I MHC (HLA-A,B,C) expression on HUVEC in a concentration-dependent manner. Optimal augmentation, approximately sixfold compared with control, was seen with 10 micrograms/ml of LPS. Time-course experiments indicated that the augmentation was maximal on Day 4. In contrast, LPS had no effect on the induction of class II MHC (HLA-DR) molecules and at concentrations higher than 0.01 micrograms/ml inhibited the interferon-gamma(IFN-gamma)-induced class II MHC expression. The inhibition was about 60% at the concentration of 100 micrograms/ml of LPS. Interleukin-1 (IL-1) had a similar effect as LPS on class I and II MHC expression. However, LPS appeared to affect MHC expression directly and not through production of IL-1 or cyclo-oxygenase pathway products, since anti-IL-1 antibodies or an inhibitor of cyclo-oxygenase pathway products, indomethacin, failed to reverse the effects of LPS. These data stress the role of LPS as a direct modulatory factor of class I and II MHC expression on endothelial cells during the development of immune and inflammatory response against Gram-negative bacteria.
Saccadometry: the possible application of latency distribution measurement for monitoring concussion (2007)

Premature return to play after concussion may have debilitating or even fatal consequences. Computerised neuropsychological test batteries are widely used to monitor recovery, but none meet all specified criteria. One possible alternative is to measure saccadic reaction time or latency. Latency reflects the operation of cerebral decision mechanisms, and is strongly influenced by many agents that impair cortical function. A portable, micro-miniature device (saccadometer) was used to record the eye movements of amateur boxers before and after competitive bouts. Individual latency distributions were significantly affected after blows to the head, though the effects seemed to be reversible, with recovery over a few days. This quantitative, objective and easy to use technique should perhaps be deployed more widely to evaluate its potential in monitoring the effects of sports-related head injuries.
Liver angiogenesis as a risk factor for hepatocellular carcinoma development in hepatitis C virus cirrhotic patients (2007)

Liver angiogenesis has a role for in HCV-related liver carcinogenesis and for defining patients at higher risk.
Disorders of Phagocyte Chemotaxis (1980)

Recent advances in understanding the physiologic and biochemical bases for recruitment of phagocytes to inflammatory sites has led to the recognition of patients who have recurrent infections because of abnormalities of phagocyte chemotaxis. In some of these patients there is abnormal chemoattractant mediator production or regulation, whereas in others there are defects in phagocytic cell function. The cellular defects in chemotaxis can be characterized as either intrinsic defects of the cellular motility apparatus or acquired defects from mediators influencing cell function or from shifts in circulating phagocyte subpopulations. Systematic study of these defects has resulted in functional, biochemical, and ultrastructural characterization of abnormal phagocyte chemotaxis in certain patients, and in some patients study has led to rational approaches for treatment. Clinical trials assessing the efficacy of such pharmacologic agents are underway.
Transgenic maize plants by tissue electroporation. (1992)

In this paper, we describe the transformation of regenerable maize tissues by electroporation. In many maize lines, immature zygotic embryos can give rise to embryogenic callus cultures from which plants can be regenerated. Immature zygotic embryos or embryogenic type I calli were wounded either enzymatically or mechanically and subsequently electroporated with a chimeric gene encoding neomycin phosphotransferase (neo). Transformed embryogenic calli were selected from electroporated tissues on kanamycin-containing media and fertile transgenic maize plants were regenerated. The neo gene was transmitted to the progeny of kanamycin-resistant transformants in a Mendelian fashion. This showed that all transformants were nonchimeric, suggesting that transformation and regeneration are a single-cell event. The maize transformation procedure presented here does not require the establishment of genotype-dependent embryogenic type II callus or cell suspension cultures and facilitates the engineering of new traits into agronomically relevant maize inbred lines.
IL-12 enhances the generation of tumour antigen-specific Th1 CD4 T cells duringex vivoexpansion (2004)

CD4+ T cells are essential for the immune response against cancer. Vaccination against cancer will likely only be effective at preventing growth of micrometastatic disease while adoptive T cell therapy will be better suited for eradication of bulky pre-existing disease (Knutson et al. Expert Opin Biol Ther 2002; 2:55-66). Problems with the use of adoptive T cell therapy include lack of CD4+ T cell help, low frequency of antigen-specific T cells, and lack of effective ex vivo expansion techniques. In this study, we focused on improving ex vivo expansion of CD4+ T helper cells. The effects of IL-12, along with IL-2, on the ex vivo generation of HER-2/neu antigen-specific T cells were examined. Patients were immunized with a peptide-based vaccine that contained a helper epitope, p776-790, derived from the intracellular domain of HER-2/neu. While T cell immunity to p776-790, assessed by proliferation assays, could be readily measured in short-term cultures, cell line generation by multiple in vitro stimulation with peptide and IL-2 as the only added cytokine resulted in loss of antigen-specific proliferation. The inclusion of IL-12, along with IL-2, restored antigen-specific proliferation in a dose-dependent fashion. The resulting p776-790-specific T cells responded readily to antigen by proliferating and producing type I cytokines (IFN-gamma and TNF-alpha). The increased proliferative response of the cultures was due in part to an increase in the number of HER-2/neu-specific T cells. These results suggest that IL-12 is an important cytokine for ex vivo recovery and maintenance of antigen-specific CD4+ T lymphocytes that would otherwise be lost by using IL-2 alone in combination with antigen. Furthermore, these results have important implications for ex vivo expansion of CD4+ T cell for use in anti-tumour adoptive immunotherapy.
Performance enhancement of multiuser MIMO wireless communication systems (2002)

This paper describes a new approach to the problem of enhancing the performance of a multiuser multiple-input-multiple-output (MIMO) system for communication from one base station to many mobile stations in both frequency-flat and frequency-selective fading channels. This problem arises in space-division multiplexing systems with multiple users where many independent signal streams can be transmitted in the same frequency and time slot through the exploitation of multiple antennas at both the base and mobile stations. Our new approach is based on maximizing a lower bound for the product of signal-to-interference plus noise ratio (SINR) of a multiuser MIMO system. This provides a closed-form (noniterative) solution for the antenna weights for all the users, under the constraint of fixed transmit power. Our solution is shown by simulation to have better performance than previously proposed iterative or noniterative solutions. In addition, our solution requires significantly reduced complexity over a gradient search-based method that directly optimizes the product SINRs while still maintaining similar performance. Our solution assumes channel state information is present at the base station or transmitter.
Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. (1981)

The complete 7410 nucleotide sequence of poliovirus type I genome was obtained from cloned cDNA. Double-stranded poliovirus cDNA was synthesized and inserted into the Pst I site of plasmid pBR322, and three clones were derived that together provided DNA copies of the entire poliovirus genome. Two of the clones contained inserts of 2.5 and 6.5 kilobases and represented all but the 5' 115 bases of poliovirus RNA. A third clone was generated from primer-extended DNA and contained sequences from the 5' end of the viral RNA. An open reading frame that was identified in the nucleotide sequence starting 743 bases from the 5' end of the RNA and extending to a termination codon 71 bases from the 3' end contained known poliovirus polypeptide sequence.
Critical Role of Connexin 43 in Secondary Expansion of Traumatic Spinal Cord Injury (2012)

Spinal cord injury (SCI) is often complicated by secondary injury as a result of the innate inflammatory response to tissue trauma and swelling. Previous studies have shown that excessive ATP release from peritraumatic regions contributes to the inflammatory response to SCI by activation of low-affinity P2X7 receptors. Because connexin hemichannels constitute an important route for astrocytic ATP release, we here evaluated the impact on post-traumatic ATP release of deletion of connexins (Cx30/Cx43) in astrocytes. In vivo bioluminescence imaging showed a significant reduction in ATP release after weight-drop injury in mice with deletion of Cx43 compared with Cx43-expressing littermates, both on a Cx30 knockout background. Moreover, astrogliosis and microglia activation were reduced in peritraumatic areas of those mice lacking Cx43; motor recovery was also significantly improved, and the traumatic lesion was smaller. Combined, these observations are consistent with a contribution by astrocytic hemichannels to post-traumatic ATP release that aggravates secondary injury and restrains functional recovery after experimental spinal cord injury. Connexins may thereby constitute a new therapeutic target in spinal cord injury.
Response to Propranolol and Diazepam in Somatic and Psychic Anxiety (1974)

A total of 12 chronically anxious psychiatric outpatients were treated with racemic propranolol (Inderal), diazepam (Valium), and placebo for one week each, using a balanced cross-over experimental design. Six patients had predominantly somatic anxiety, complaining mostly of bodily symptoms, and six had mainly psychic anxiety, complaining primarily of psychological symptoms. Clinical ratings of anxiety were made by patient and psychiatrist after each treatment. Though diazepam was in general more effective than propranolol or placebo in relieving anxiety, propranolol was more effective than placebo in patients with somatic anxiety but not in those with psychic anxiety. We suggest that propranolol should be reserved for patients whose anxiety symptoms are mainly somatic.
Dissecting psychiatric spectrum disorders by generative embedding (2013)

This proof-of-concept study examines the feasibility of defining subgroups in psychiatric spectrum disorders by generative embedding, using dynamical system models which infer neuronal circuit mechanisms from neuroimaging data. To this end, we re-analysed an fMRI dataset of 41 patients diagnosed with schizophrenia and 42 healthy controls performing a numerical n-back working-memory task. In our generative-embedding approach, we used parameter estimates from a dynamic causal model (DCM) of a visual-parietal-prefrontal network to define a model-based feature space for the subsequent application of supervised and unsupervised learning techniques. First, using a linear support vector machine for classification, we were able to predict individual diagnostic labels significantly more accurately (78%) from DCM-based effective connectivity estimates than from functional connectivity between (62%) or local activity within the same regions (55%). Second, an unsupervised approach based on variational Bayesian Gaussian mixture modelling provided evidence for two clusters which mapped onto patients and controls with nearly the same accuracy (71%) as the supervised approach. Finally, when restricting the analysis only to the patients, Gaussian mixture modelling suggested the existence of three patient subgroups, each of which was characterised by a different architecture of the visual-parietal-prefrontal working-memory network. Critically, even though this analysis did not have access to information about the patients' clinical symptoms, the three neurophysiologically defined subgroups mapped onto three clinically distinct subgroups, distinguished by significant differences in negative symptom severity, as assessed on the Positive and Negative Syndrome Scale (PANSS). In summary, this study provides a concrete example of how psychiatric spectrum diseases may be split into subgroups that are defined in terms of neurophysiological mechanisms specified by a generative model of network dynamics such as DCM. The results corroborate our previous findings in stroke patients that generative embedding, compared to analyses of more conventional measures such as functional connectivity or regional activity, can significantly enhance both the interpretability and performance of computational approaches to clinical classification.
Nematic twist-bend phase with nanoscale modulation of molecular orientation (2013)

A state of matter in which molecules show a long-range orientational order and no positional order is called a nematic liquid crystal. The best known and most widely used (for example, in modern displays) is the uniaxial nematic, with the rod-like molecules aligned along a single axis, called the director. When the molecules are chiral, the director twists in space, drawing a right-angle helicoid and remaining perpendicular to the helix axis; the structure is called a chiral nematic. Here using transmission electron and optical microscopy, we experimentally demonstrate a new nematic order, formed by achiral molecules, in which the director follows an oblique helicoid, maintaining a constant oblique angle with the helix axis and experiencing twist and bend. The oblique helicoids have a nanoscale pitch. The new twist-bend nematic represents a structural link between the uniaxial nematic (no tilt) and a chiral nematic (helicoids with right-angle tilt).
Carbonic anhydrase inhibitors (2002)

At least 14 different carbonic anhydrase (CA, EC 4.2.1.1) isoforms were isolated in higher vertebrates, where these zinc enzymes play crucial physiological roles. Some of these isozymes are cytosolic (CA I, CA II, CA III, CA VII), others are membrane-bound (CA IV, CA IX, CA XII, and CA XIV), CA V is mitochondrial and CA VI is secreted in saliva. Three acatalytic forms are also known, which are denominated CA related proteins (CARP), CARP VIII, CARP X, and CARP XI. Several important physiological and physio-pathological functions are played by many CA isozymes, which are strongly inhibited by aromatic and heterocyclic sulfonamides as well as inorganic, metal complexing anions. The catalytic and inhibition mechanisms of these enzymes are understood in detail, and this helped the design of potent inhibitors, some of which possess important clinical applications. The use of such enzyme inhibitors as antiglaucoma drugs will be discussed in detail, together with the recent developments that led to isozyme-specific and organ-selective inhibitors. A recent discovery is connected with the involvement of CAs and their sulfonamide inhibitors in cancer: several potent sulfonamide inhibitors inhibited the growth of a multitude of tumor cells in vitro and in vivo, thus constituting interesting leads for developing novel antitumor therapies. Furthermore, some other classes of compounds that interact with CAs have recently been discovered, some of which possess modified sulfonamide or hydroxamate moieties. Some sulfonamides have also applications as diagnostic tools, in PET and MRI or as antiepileptics or for the treatment of other neurological disorders. Future prospects for drug design applications for inhibitors of these ubiquitous enzymes are also discussed.