gebhart/patrepeval huggingface dataset:
Passive Immunity in Prevention and Treatment of Infectious Diseases (2000)

Antibodies have been used for over a century in the prevention and treatment of infectious disease. They are used most commonly for the prevention of measles, hepatitis A, hepatitis B, tetanus, varicella, rabies, and vaccinia. Although their use in the treatment of bacterial infection has largely been supplanted by antibiotics, antibodies remain a critical component of the treatment of diptheria, tetanus, and botulism. High-dose intravenous immunoglobulin can be used to treat certain viral infections in immunocompromised patients (e.g., cytomegalovirus, parvovirus B19, and enterovirus infections). Antibodies may also be of value in toxic shock syndrome, Ebola virus, and refractory staphylococcal infections. Palivizumab, the first monoclonal antibody licensed (in 1998) for an infectious disease, can prevent respiratory syncytial virus infection in high-risk infants. The development and use of additional monoclonal antibodies to key epitopes of microbial pathogens may further define protective humoral responses and lead to new approaches for the prevention and treatment of infectious diseases.
Kdm6a Deficiency Activates Inflammatory Pathways, Promotes M2 Macrophage Polarization, and Causes Bladder Cancer in Cooperation with p53 Dysfunction (2020)

Our findings provide insights into multistep carcinogenic processes of bladder cancer and suggest molecular targeted therapeutic approaches for patients with bladder cancer with <i>KDM6A</i> dysfunction.
Exploiting short-lived variables in superscalar processors (1995)

In this paper we present experimental evidence showing that a significant number of program variables are short-lived in the sense that their live ranges span only a few instructions. In dynamically scheduled superscalar processors using mechanisms like the reorder buffer, the live ranges for these short-lived variables may occur entirely within the reorder buffer. Therefore, there should be no need to retire (commit) the values produced by these live ranges to the register file. On the basis of this observation, we have proposed a scheme that includes a compiler analysis and a simple architecture extension to avoid the useless commits of the values generated for these short-lived variables. Moreover we have proposed an extension to the existing register allocation mechanism that does not assign these short-lived variables to locations in the register file. Analyses and results are presented.
Promoter library designed for fine-tuned gene expression in Pichia pastoris (2008)

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (P(AOX1)) sequence. This first library initially spanned an activity range between approximately 6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing a green fluorescent protein (GFP) variant, the new regulatory toolbox was successfully utilized in a 'real case', i.e. the expression of industrial enzymes. Characterization of the library under repressing, derepressing and inducing conditions displayed at least 12 cis-acting elements involved in P(AOX1)-driven high-level expression. Based on this deletion analysis, novel short artificial promoter variants were constructed by combining cis-acting elements with basal promoter. In addition to improving yields and quality of heterologous protein production, the new P(AOX1) synthetic promoter library constitutes a basic toolbox to fine-tune gene expression in metabolic engineering and sequential induction of protein expression in synthetic biology.
Portable two-color in vivo flow cytometer for real-time detection of fluorescently-labeled circulating cells (2007)

The recent introduction of the in vivo flow cytometer for real-time, noninvasive detection and quantification of cells circulating in the vasculature of small animals has provided a powerful tool for tracking the roles of different types of cells in disease progression. We describe a portable version of the device, which provides the capability to: a) excite and detect fluorescence at two distinct colors simultaneously, and b) perform data analysis in real time. These advances improve significantly the utility of the instrument and provide a means of increasing detection specificity. As examples, we present the depletion kinetics of circulating green fluorescent protein (GFP)-labeled breast cancer cells in the vasculature of mice, and the specific detection of circulating hematopoietic stem cells labeled in vivo with two antibodies.
The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis (2019)

Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens-a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
On the biological relevance of MHC class II and B7 expression by tumour cells in melanoma metastases (2003)

A large number of studies have indicated that specific immune reactivity plays a crucial role in the control of malignant melanoma. In this context, expression of MHC I, MHC II and B7 molecules by melanoma cells is seen as relevant for the immune response against the tumour. For a better understanding of the biological relevance of MHC II and B7 expression by tumour cells in metastatic melanoma, we studied the expression of these molecules in melanoma metastases in relation to the inflammatory response, regression of the tumour and survival from 27 patients treated with biochemotherapy (30 mg m(-2) Cisplatin and 250 mg m(-2) decarbazine (dimethyl-triazene-imidazole-carboxamide, DTIC) on days 1-3 i.v., and 10(7) IU IFN-alpha 2b 3 days a week s.c., q. 28d). In 19 out of 27 lesions studied, we found expression of MHC II by the tumour cells, while only in one out of 11 tumour biopsies obtained from untreated metastatic melanoma patients, MHC II expression was detected. Expression of B7.1 and B7.2 by tumour cells was found in nine out of 24 and 19 out of 24 lesions, respectively. In all cases where B7.1 expression was found, expression of B7.2 by the tumour cells was also seen. In general, no or only few inflammatory cells positive for B7 were found. Expression of MHC II by tumour cells was positively correlated with the presence of tumour-infiltrating lymphocytes, regression of the lesion, and with time to progression (TTP) and overall survival (OS) of the patient. However, no significant correlation between B7.1 or B7.2 expression and regression of the tumour, TTP or OS was found. In light of other recent findings, these data altogether do support a role as biomarker for MHC II expression by tumour cells; however, its exact immunological pathomechanism(s) remain to be established.
Reduced Frameshift Fidelity and Processivity of HIV-1 Reverse Transcriptase Mutants Containing Alanine Substitutions in Helix H of the Thumb Subdomain (1995)

We have analyzed two human immunodeficiency virus (HIV-1) reverse transcriptase mutants of helix H in the thumb subdomain suggested by x-ray crystallography to interact with the primer strand of the template-primer. These enzymes, G262A and W266A, were previously shown to have greatly elevated dissociation rate constants for template-primer and to be much less sensitive to inhibition by 3'-azidodeoxythymidine 5'-triphosphate. Here we describe their processivity and error specificity. The results reveal that: (i) both enzymes have reduced processivity and lower fidelity for template-primer slippage errors, (ii) they differ from each other in sequence-dependent termination of processive synthesis and in error specificity, and (iii) the magnitude of the mutator effect relative to wild-type enzyme for deletions in homopolymeric sequences decreases as the length of the run increases. Thus amino acid substitutions in a subdomain thought to interact with the duplex template-primer confer a strand slippage mutator phenotype to a replicative DNA polymerase. This suggests that interactions between specific amino acids and the primer stem at positions well removed from the active site are critical determinants of processivity and fidelity. These effects, obtained in aqueous solution during catalytic cycling, are consistent with and support the existing crystallographic structural model.
Treatment of Attention-Deficit–Hyperactivity Disorder (1999)

Attention-deficit–hyperactivity disorder (ADHD) is a common but controversial syndrome characterized by developmentally inappropriate hyperactivity, impulsivity, and inattention.1 The disorder, which continues throughout life,27 usually begins in childhood and is characterized by excessive activity, even when adjusted for developmental level, and limited behavioral control. A severely affected child, in whom behavioral control is absent, is exhausting to care for.ADHD is controversial despite the acceptance of specific diagnostic criteria. That it is an extreme form of commonly occurring types of behavior rather than a disorder with discrete determinants is suggested by genetic studies, including a large study of twins, in . . .
Device Physics of Solution‐Processed Organic Field‐Effect Transistors (2005)

Abstract Field‐effect transistors based on solution‐processible organic semiconductors have experienced impressive improvements in both performance and reliability in recent years, and printing‐based manufacturing processes for integrated transistor circuits are being developed to realize low‐cost, large‐area electronic products on flexible substrates. This article reviews the materials, charge‐transport, and device physics of solution‐processed organic field‐effect transistors, focusing in particular on the physics of the active semiconductor/dielectric interface. Issues such as the relationship between microstructure and charge transport, the critical role of the gate dielectric, the influence of polaronic relaxation and disorder effects on charge transport, charge‐injection mechanisms, and the current understanding of mechanisms for charge trapping are reviewed. Many interesting questions on how the molecular and electronic structures and the presence of defects at organic/organic heterointerfaces influence the device performance and stability remain to be explored.
Catalysis of peptide dissociation from class II MHC-peptide complexes (1999)

Certain peptides such as dynorphin A [dynA-(1-13)] enhance the release of antigenic peptides bound to class II MHC molecules at neutral pH. This enhanced release has been termed push off. Previous work has shown that the antigenic pigeon cytochrome c peptide PCC-(89-104) has at least two conformational isomers when bound to the class II MHC protein I-Ek. We have accordingly studied the push off of PCC-(89-104) from the complex PCC-(89-104)/I-Ek to see whether these isomeric conformations are distinguished by the push-off effect. A comparison of the association and dissociation kinetics of PCC-(89-104)/I-Ek in the presence of dynA-(1-13) shows that dynA-(1-13) does not simply replace PCC-(89-104) but rather acts catalytically. The major product is peptide-free I-Ek, which is receptive to further peptide binding. Evidence is presented that a two peptide-one MHC complex is formed in solution. This ternary complex represents the first step of the mechanism of push off. 19F NMR data are presented that indicate that dynA-(1-13) interacts specifically with only one of the two isomeric complexes of PCC-(89-104) and I-Ek. A push-off mechanism is proposed in which dynA-(1-13) binds outside the peptide binding groove. In a second step, the dissociation of one of the two isomers is specifically enhanced. Thus the push-off effect may be useful for identifying conformational isomers and for separating them.
Vascular endothelial growth factor stimulates prostacyclin production and activation of cytosolic phospholipase A2 in endothelial cells via p42/p44 mitogen‐activated protein kinase (1997)

Vascular endothelial growth factor (VEGF) stimulated a time- and concentration-dependent increase in PGI2 synthesis in human umbilical vein endothelial cells with a mean maximum increase of 2-fold above basal levels at 25 ng/ml after 60 min. VEGF also rapidly stimulated the release of arachidonic acid and phosphorylation and activation of cytosolic phospholipase A2 (cPLA2). The VEGF-related factor, placenta growth factor (PIGF), had little effect on PGI2 synthesis, arachidonic acid release or cPLA2 activation. PD98059, a selective inhibitor of MAP kinase kinase, caused complete inhibition of VEGF-stimulated MAP kinase activity, PGI2 synthesis and cPLA2 gel retardation, but had no effect on VEGF-induced vWF secretion. These findings provide the first evidence that VEGF can stimulate PGI2 synthesis via cPLA2-mediated arachidonic acid release and indicate that VEGF stimulation of this biosynthetic pathway may occur, at least in part, via activation of p42/p44 MAP kinases.
Validation of the Excited Component of the Positive and Negative Syndrome Scale (PANSS-EC) in a naturalistic sample of 278 patients with acute psychosis and agitation in a psychiatric emergency room (2011)

The factorial analyses confirm the unifactorial structure of the PANSS-EC subscale. The PANSS-EC showed a strong linear correlation with rating scales such as CGI-S and ACES. PANSS-EC has also shown an excellent capacity to detect real changes in agitated patients.
Linkage of cystic fibrosis to two tightly linked DNA markers: joint report from a collaborative study. (1986)

A collaborative study involving seven research groups provided an opportunity to investigate the linkage relationships between cystic fibrosis and two DNA marker loci, MET and pJ3.11 (D7S8), on an extended sample of 211 tested families. The maximum lod scores, recombination estimates, and confidence upper bounds (in parentheses) were 91.0 at theta = .004 (.012) for CF and MET, 71.3 at theta = .003 (.011) for CF and D7S8, and 69.3 at theta = .018 (.036) for MET and D7S8. Three-locus analyses yielded best support for the order MET-CF-D7S8, with odds against the alternate orders CF-MET-D7S8 and CF-D7S8-MET of 9:1 and 161:1, respectively. However, the number of observed recombinants was small and only one of the recombinants was jointly informative for all three markers. Significant allelic association was found between CF and both MET and D7S8. Weaker association between the latter two loci is consistent with the order MET-CF-D7S8.
Manufacturing Issues Related to Combining Different Antigens: An Industry Perspective (2001)

Despite the growing demand for combination vaccines, many challenges have been encountered in developing them. It is difficult to predict the physical compatibility and stability of antigens in combination, because these characteristics are highly dependent on vaccine excipients. Clinical evaluation of potential modifications of efficacy of antigens in combination may be alleviated by use of appropriate animal models. Manufacturing issues, such as batch-release testing, storage of intermediate products, and the shift to preservative-free products, are of particular concern because they have the potential to affect the supply chain. Managing changes in the manufacture of one antigen that is a component of several different combination vaccines is also difficult. However, most potential issues can be resolved through the simplification of regulatory processes and harmonization of requirements, such as the acceptance of comparability protocols and antigen master files. Continued collaboration between industry and authorities is necessary to develop effective means of handling all submissions pertaining to combination vaccines.
Epitope Mapping of the Immunodominant Antigen TB10.4 and the Two Homologous Proteins TB10.3 and TB12.9, Which Constitute a Subfamily of the esat-6 Gene Family (2002)

The human T-cell recognition of the low-molecular-mass culture filtrate antigen TB10.4 was evaluated in detail. The molecule was strongly recognized by T cells isolated from tuberculosis (TB) patients and from BCG-vaccinated donors. The epitopes on TB10.4 were mapped with overlapping peptides and found to be distributed throughout the molecule. The broadest response was found in TB patients, whereas the response in BCG-vaccinated donors was focused mainly toward a dominant epitope located in the N terminus (amino acids 1 to 18). The gene encoding TB10.4 was found to belong to a subfamily within the esat-6 family that consists of the three highly homologous proteins TB10.4, TB10.3, and TB12.9 (Rv0288, Rv3019c, and Rv3017c, respectively). Southern blot analysis combined with database searches revealed that the three members of the TB10.4 family were present only in strains of the Mycobacterium tuberculosis complex, including BCG, and M. kansasii, whereas other atypical mycobacteria had either one (M. avium, M. intracellulare, and M. marinum) or none (M. scrofulaceum, M. fortuitum, and M. szulgai) of the genes. The fine specificity of the T-cell response to the three closely related esat-6 family members was markedly different, with only a few epitopes shared between the molecules. Minimal differences in the amino acid sequence translated into large differences in recognition by T cells and secretion of gamma interferon. In general, the peptides from TB10.4 stimulated the largest responses, but epitopes unique to both TB10.3 and TB12.9 were found. The relevance of the findings for TB vaccine development and as a potential mechanism for immune evasion is discussed.
DSM-IV: Diagnostic and Statistical Manual of Mental Disorders (1994)

<b>Diagnostic Criteria From DSM-IV,</b>by the American Psychiatric Association, 358 pp, spiral-bound, $22.50, ISBN 0-89042-064-5, Washington, DC, American Psychiatric Press Inc, 1994. <i>DSM-IV Sourcebook</i>, vol 1, edited by Thomas A. Widiger, Allen J. Frances, Harold Alan Pincus, Michael B. First, Ruth Ross, and Wendy Davis, 768 pp, $112.50, ISBN 0-89042-065-3, Washington, DC, American Psychiatric Association, 1994. <i>DSM-IV: Diagnostic and Statistical Manual of Mental Disorders</i>, fourth edition, was developed with a great deal of input from mental health professionals and professional organizations. In addition, there was a significant collaboration between the American Psychiatric Association (APA) and the World Health Organization, as it developed the tenth revision of the<i>International Statistical Classification of Diseases and Related Health Problems (ICD-10)</i>. As a result, DSM-IV is a great improvement over the third edition<i>(DSM-III)</i>and the third edition, revised<i>(DSM-III-R)</i>. The Task Force on<i>DSM-IV</i>and 13 work groups (each responsible for a section
Specification of Distinct Dopaminergic Neural Pathways: Roles of the Eph Family Receptor EphB1 and Ligand Ephrin-B2 (1999)

Dopaminergic neurons in the substantia nigra and ventral tegmental area project to the caudate putamen and nucleus accumbens/olfactory tubercle, respectively, constituting mesostriatal and mesolimbic pathways. The molecular signals that confer target specificity of different dopaminergic neurons are not known. We now report that EphB1 and ephrin-B2, a receptor and ligand of the Eph family, are candidate guidance molecules for the development of these distinct pathways. EphB1 and ephrin-B2 are expressed in complementary patterns in the midbrain dopaminergic neurons and their targets, and the ligand specifically inhibits the growth of neurites and induces the cell loss of substantia nigra, but not ventral tegmental, dopaminergic neurons. These studies suggest that the ligand-receptor pair may contribute to the establishment of distinct neural pathways by selectively inhibiting the neurite outgrowth and cell survival of mistargeted neurons. In addition, we show that ephrin-B2 expression is upregulated by cocaine and amphetamine in adult mice, suggesting that ephrin-B2/EphB1 interaction may play a role in drug-induced plasticity in adults as well.
Cutting Edge: NKG2D-Dependent Cytotoxicity Is Controlled by Ligand Distribution in the Target Cell Membrane (2011)

Although the importance of membrane microdomains in receptor-mediated activation of lymphocytes has been established, much less is known about the role of receptor ligand distribution on APC and target cells. Detergent-resistant membrane domains, into which GPI-linked proteins partition, are enriched in cholesterol and glycosphingolipids. ULBP1 is a GPI-linked ligand for natural cytotoxicity receptor NKG2D. To investigate how ULBP1 distribution on target cells affects NKG2D-dependent NK cell activation, we fused the extracellular domain of ULBP1 to the transmembrane domain of CD45. Introduction of this transmembrane domain eliminated the association of ULBP1 with the detergent-resistant membrane fraction and caused a significant reduction of cytotoxicity and degranulation by NK cells. Clustering and lateral diffusion of ULBP1 was not affected by changes in the membrane anchor. These results show that the partitioning of receptor ligands in discrete membrane domains of target cells is an important determinant of NK cell activation.
Collection, processing and storage of peripheral blood stem cells (PBSC). (1991)

Eight patients with hematological malignancies were treated with autologous blood stem cell transplantation (ABSCT). Hemopoietic precursor cells were mobilized into the peripheral blood (PB) by chemotherapeutic induction of transient myelosuppression followed by an overshooting of blood stem cell concentration. PB CFU-GM showed a 15-20 fold increase on days 15-20 after chemotherapy. Peripheral blood stem cells were collected by 5-8 continuous flow leukaphereses using a Fenwall CS 3000 blood cell separator when platelet and WBC count was rising rapidly (platelet greater than 50 x 10e9/L and WBC greater than 1 x 10e9/L). Mean CFU-GM collected per run by leukapheresis were 10.85 x 10e4/Kg (procedure 3), 10.03 x 10e4/Kg (modified procedure 1). Mononuclear cell suspension in 10% DMSO was frozen at controlled rate freezer (-1 degree C to -4 degrees C) and stored in the liquid phase of nitrogen. After thawing CFU-GM recoveries ranged from 13.8% to 81.5%; 55-70% of recovered cells excluded trypan blue dye.