gebhart/patrepeval huggingface dataset:
Establishment of Male and Female Nuclear Transfer Embryonic Stem Cell Lines from Different Mouse Strains and Tissues1 (2004)

Nuclear transfer can be used to generate embryonic stem cell lines from somatic cells, and these have great potential in regenerative medicine. However, it is still unclear whether any individual or cell type can be used to generate such lines. Here, we tested seven different male and female mouse genotypes and three cell types as sources of nuclei to determine the efficiency of establishing nuclear transfer embryonic stem cell lines. Lines were successfully established from all sources. Cumulus cell nuclei from F(1) mouse genotypes showed a significantly higher cumulative establishment rate from reconstructed oocytes than from other cells; however, there were no genotype differences in success rates from cloned blastocysts. Thus, the overall success depends on preimplantation development, and, once embryos have reached the blastocyst stage, the genotype differences disappear. All mouse genotypes that were tested demonstrated at least one cell line that subsequently contributed to germline transmission in chimeric mice, so these cell lines clearly possess the same potential as embryonic stem cells derived from fertilized embryos. Thus, nuclear transfer embryonic stem cells can be generated relatively easily from a variety of inbred mouse genotypes and cell types of both sexes, even though it may be more difficult to generate clones directly.
Genetic reprogramming in pathways of colonic cell maturation induced by short chain fatty acids: comparison with trichostatin A, sulindac, and curcumin and implications for chemoprevention of colon cancer. (2000)

The short-chain fatty acid butyrate, produced by microbial fermentation of dietary fiber in the large intestine, is a physiological regulator of major pathways of colonic epithelial cell maturation: cell cycle arrest, lineage-specific differentiation, and apoptosis. Microarray analysis of 8,063 sequences demonstrated a complex cascade of reprogramming of SW620 colonic epithelial cells upon treatment with butyrate characterized by the progressive recruitment of gene sets as a function of time. Comparison with the effects of trichostatin A, in conjunction with differences in the kinetics of alteration of histone acetylation induced by butyrate and trichostatin A, identified subsets of induced and repressed genes likely coordinately regulated by altered histone acetylation. The butyrate response was also compared in detail with that of sulindac, a nonsteroidal anti-inflammatory drug with significant chemopreventive activity for colon cancer, and curcumin, a component of mustard and curry structurally and functionally related to sulindac that also has chemopreventive activity. Although gene clusters were identified that showed similar responses to butyrate and sulindac, the data were characterized by the extensive differences in the effects of the two agents. This was striking for functional classes of genes involved in signaling pathways and in cell cycle progression, although butyrate and sulindac induce a similar G0-G1 arrest, elevation of beta-catenin-Tcf signaling, and apoptotic cascade. As regards cell cycle arrest, the underlying mechanism in response to butyrate was most similar to that of the Caco-2 cell line that had spontaneously undergone a G0-G1 arrest and least similar to the G2-M arrest stimulated by curcumin. Thus, high-throughput microarray analysis of gene expression profiles can be used to characterize and distinguish the mechanisms of response of colonic epithelial cells to physiological and pharmacological inducers of cell maturation. This has important implications for characterization of chemopreventive agents and recognition of potential toxicity and synergies. The data bases, gene clusters, and analyses are available at http:// sequence.aecom.yu.edu/genome/.
Thiol-ene “click” reactions and recent applications in polymer and materials synthesis (2009)

This review highlights examples of recent applications of both the radical-mediated and base/nucleophile-initiated thiol-ene reactions in polymer and materials synthesis. Initial discussion focuses on mechanistic aspects of these reactions and also notes some of the structural considerations, with respect to reactants, that should be considered when practising such chemistries. The review is not intended to be exhaustive but rather to serve as an illustration of the impressive versatility and clear potential of these thiol-based “click” reactions and to highlight examples demonstrating its broad utility.
A microbial platform for renewable propane synthesis based on a fermentative butanol pathway (2015)

This study expands the metabolic toolbox for renewable propane production and provides new insight and understanding for the development of next-generation biofuel platforms. In developing an alternative CoA-dependent fermentative butanol pathway, which includes an engineered ADO variant (ADOA134F), the study addresses known limitations, including the low bio-availability of butyraldehyde precursors and poor activity of ADO with butyraldehyde. Graphical abstractPropane synthesis derived from a fermentative butanol pathway is enabled by metabolic engineering.
Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types (2012)

Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.
Nephrotoxicity of sodium valproate and protective role of L-cysteine in rats at biochemical and histological levels (2016)

The concurrent administration of LC with SV significantly had beneficial effects on the kidney and all the above parameters have been improved.
Staphylococcus aureusPneumonia: Emergence of MRSA in the Community (2005)

The clinical presentation of staphylococcal pneumonia is changing. Healthy young people without traditional risk factors for Staphylococcus aureus disease are presenting with severe necrotizing infection and high mortality. The clinical picture is reminiscent of outbreaks of postinfluenzal staphylococcal pneumonia seen in the past century. Most of these staphylococcal strains are methicillin-resistant and are not health care associated. Many strains contain toxins that are likely responsible for the severity of illness seen. Panton-Valentine leukocidin has rarely been identified in S. aureus until recently. It appears that the genetic element for methicillin resistance has been introduced into multiple highly virulent methicillin-susceptible strains with great potential for further spread. Early recognition and treatment of possible community-acquired methicillin-resistant S. aureus (CA-MRSA) is essential. It is equally important to attain microbiological confirmation of the diagnosis for optimal treatment and to initiate appropriate infection control procedures.
Genotype and psychological phenotype in tuberous sclerosis (2004)

Tuberous sclerosis complex (TSC, MIM 191090 and 191100) is an autosomal dominant, multisystem disorder characterised by the development of a variety of hamartomatous growths.1 The TSC phenotype includes renal involvement (in over 80% of patients) with angiomyolipomas and cysts; skin involvement with facial angiofibromas, hypomelanotic macules, shagreen patches, and periungual fibromas; and cardiac, ophthalmic, and pulmonary involvement. Many of the frequent and serious complications of TSC, including epilepsy, mental retardation, and a wide range of psychiatric and behavioural disorders, reflect the cerebral involvement that occurs in over 90% of cases. Structural abnormalities in the brain include: cortical tubers that are localised areas of loss of normal hexalaminar cortical organisation, and that contain abnormal and enlarged cells categorised as cytomegalic neurones and balloon cells; subependymal nodules that are localised proliferations of abnormal cells in the periventricular zone; and migration tracts through the white matter linking subependymal and cortical lesions.

Mental retardation is estimated to occur in approximately 45% of cases.2 It is virtually always associated with a history of seizures correlated with early seizure onset, poor seizure control, and type of seizure at onset with the greatest risk for infantile spasms.3 The association between mental retardation and infantile spasms is particularly strong in the context of TSC.4 People with TSC are also reported to have high rates of autistic disorder, attention deficit hyperactivity disorder (ADHD), and sleep disorder. Although autistic disorder is a feature of several genetic disorders of childhood, its frequency is highest in TSC,5 and the strength of the association does not appear to be explained simply by the frequency of infantile spasms in TSC.6 Sleep disorder in TSC is associated with the presence of other behavioural problems and can be exacerbated by nocturnal seizures.7,8 There are also anecdotal reports of …
FANCD2 re-expression is associated with glioma grade and chemical inhibition of the Fanconi Anaemia pathway sensitises gliomas to chemotherapeutic agents (2014)

Brain tumours kill more children and adults under 40 than any other cancer. Around half of primary brain tumours are glioblastoma multiforme (GBMs) where treatment remains a significant challenge, where survival rates have improved little over the last 40 years, thus highlighting an unmet need for the identification/development of novel therapeutic targets and agents to improve GBM treatment. Using archived and fresh glioma tissue, we show that in contrast to normal brain or benign schwannomas GBMs exhibit re-expression of FANCD2, a key protein of the Fanconi Anaemia (FA) DNA repair pathway, and possess an active FA pathway. Importantly, FANCD2 expression levels are strongly associated with tumour grade, revealing a potential exploitable therapeutic window to allow inhibition of the FA pathway in tumour cells, whilst sparing normal brain tissue. Using several small molecule inhibitors of the FA pathway in combination with isogenic FA-proficient/deficient glioma cell lines as well as primary GBM cultures, we demonstrate that inhibition of the FA pathway sensitises gliomas to the chemotherapeutic agents Temozolomide and Carmustine. Our findings therefore provide a strong rationale for the development of novel and potent inhibitors of the FA pathway to improve the treatment of GBMs, which may ultimately impact on patient outcome.
Combining Multiple Comparisons and Modeling Techniques in Dose‐Response Studies (2005)

The analysis of data from dose-response studies has long been divided according to two major strategies: multiple comparison procedures and model-based approaches. Model-based approaches assume a functional relationship between the response and the dose, taken as a quantitative factor, according to a prespecified parametric model. The fitted model is then used to estimate an adequate dose to achieve a desired response but the validity of its conclusions will highly depend on the correct choice of the a priori unknown dose-response model. Multiple comparison procedures regard the dose as a qualitative factor and make very few, if any, assumptions about the underlying dose-response model. The primary goal is often to identify the minimum effective dose that is statistically significant and produces a relevant biological effect. One approach is to evaluate the significance of contrasts between different dose levels, while preserving the family-wise error rate. Such procedures are relatively robust but inference is confined to the selection of the target dose among the dose levels under investigation. We describe a unified strategy to the analysis of data from dose-response studies which combines multiple comparison and modeling techniques. We assume the existence of several candidate parametric models and use multiple comparison techniques to choose the one most likely to represent the true underlying dose-response curve, while preserving the family-wise error rate. The selected model is then used to provide inference on adequate doses.
Streamlined analysis schema for high-throughput identification of endogenous protein complexes (2010)

Immunoprecipitation followed by mass spectrometry (IP/MS) has recently emerged as a preferred method in the analysis of protein complex components and cellular protein networks. Targeting endogenous protein complexes of higher eukaryotes, particularly in large-scale efforts, has been challenging due to cellular heterogeneity, high proteome complexity, and, compared to lower organisms, lack of efficient in-locus epitope-tagging techniques. It is further complicated by variability in nonspecific identifications and cross-reactivity of primary antibodies. Still, the study of endogenous human protein networks is highly desired despite its challenges. Here we describe a streamlined IP/MS protocol for the purification and identification of extended endogenous protein complexes. We investigate the sources of nonspecific protein binding and develop semiquantitative specificity filters that are based on peptide spectral count measurements. We also outline logical constraints for the derivation of accurate complex composition from IP/MS data and demonstrate the effectiveness of this approach by presenting our analyses of different transcriptional coregulator complexes. We show consistent purification of novel components for the Integrator complex, analyze the composition of the Mediator complex solely from our data to demonstrate the wide usability of spectral counts, and deconvolute heterogeneous HDAC1/2 networks into core complex modules and several novel subcomplex interactions.
High aspect ratio microelectromechanical systems: A versatile approach using carbon nanotubes as a framework (2009)

We recently developed a fabrication process for carbon nanotube templated MEMS. The fabrication process involves growing a three dimensional pattern from carbon nanotube forests and filling that forest by chemical vapor infiltration to make a solid structure. This templating process allows us to fabricate extremely high aspect ratio microscale structures from a wide variety of materials. The nanotube structures can be hundreds of microns tall with lateral pattern dimensions down to a few microns. The chemical vapor infiltration has been shown with silicon and silicon nitride but could be extended to many other materials. In this paper, we investigate the microstructure of the filling material and extend the process to the fabrication of comb actuators.
Quality of Life, Physical Disability, and Respiratory Impairment in Duchenne Muscular Dystrophy (2005)

Quality of life in DMD is not correlated with physical impairment nor the need for noninvasive positive-pressure ventilation. The surprisingly high quality of life experienced by these severely disabled patients should be taken into consideration when therapeutic decisions are made.
Asynchronous sequential switching circuits with unrestricted input changes (1970)

The problem of designing asynchronous circuits where the changes in binary input signals occur independently of one another is discussed. If several input changes occur within some interval δ1, the circuit behaves as though the changes were simultaneous. If consecutive changes are spaced by intervals exceeding some longer interval δ2 then the circuit reacts as though a sequence of single changes had occurred. But when the spacing is between these values, the system may react in an unsatisfactory manner unless special attention is paid to the problem during the design process. Constraints imposed by this problem on the row assignment and on the delay elements are derived, as well as a method for computing δ1 and δ2.
Female Suicide Terrorism in South Asia: Comparing the Tamil Separatists and Kashmir Insurgents (2011)

In this article we compare two conflicts in South Asia—civil war in Sri Lanka and the insurgency in Kashmir—to investigate the enabling conditions for female suicide terrorism in the former, and the lack thereof in the latter. We conclude that female suicide terrorism is a product of several inter-related factors that feed into each other: (i) tormented society, (ii) individual grievances, and (iii) a terrorist organisation with an effective indoctrination structure. Thus, rather than focusing on the individual motivations behind the female bombers, it is important to situate them in specific socio-political contexts.
Characterization of MAX.3 antigen, a glycoprotein expressed on mature macrophages, dendritic cells and blood platelets: identity with CD84 (2000)

MAX.3 is a monoclonal antibody that preferentially reacts with mature macrophages (MAC), monocyte-derived dendritic cells, megakaryocytes and platelets. In this study, we describe the characterization, purification and identification of the MAX.3 antigen. Immunoprecipitation and SDS/PAGE revealed different molecular masses of MAX.3 antigen in MAC (60-90 kDa) and platelets (58-64 kDa), whereas a similar size (45 kDa) was observed in both cell types after digestion with N-glycosidase F. Lectin affinity and sequential treatment with different glycosidases suggests complex type glycosylation of MAX.3 antigen in MAC and hybrid type glycosylation in platelets. Amino acid sequencing led to the identification of a corresponding cDNA clone and showed its identity to the sequence of the CD84 antigen, a member of the CD2 family of cell surface molecules. MAX.3/CD84 was further studied by immunohistochemistry and a variable expression was found on tissue MAC, confirming this antigen to be mainly a marker for MAC in situ.
Fractionated radioimmunotherapy of B-cell malignancies with 131I-Lym-1. (1990)

Eighteen patients with Stage 4 B-cell malignancies, which were primarily of intermediate or high grade and progressive despite multiple drug chemotherapy and external irradiation, were treated with fractionated doses of 131I-labeled Lym-1. Lym-1 is an IgG2a monoclonal antibody that was produced by immunizing mice with Raji cell nuclei that originated from a patient with African Burkitt's lymphoma. Despite advanced disease, 10 of the patients had objective evidence for a complete or partial remission. Toxicity was very modest except in one patient who developed hypotension. Dose-dependent hepatic uptake of Lym-1 was observed in the patients and in BALB/c mice suggesting receptor-mediated recognition of this murine antibody.
Multiple model estimation using svm-based learning (2003)

Most existing learning algorithms have been developed for standard formulations of the learning problem, such as classification or regression. These standard inductive learning formulations assume that all available (or training) data can be well described by a single statistical model. For example, in classification setting the goal is to estimate a single decision boundary (which may be complex or nonlinear). Likewise, under regression formulation, the goal is to estimate a single target function from finite and noisy data samples. However, there are many applications which naturally lead to learning formulations where the goal is to estimate several models from available (finite) data. For such applications, it may be reasonable to assume that the data is generated by several (unknown) models; however we do not know which model has generated a particular sample. For example, in computer vision, a sequence of video frames may contain several moving objects (with overlapping trajectories), so the problem of multiple motion estimation can be viewed under multiple model estimation framework. For such multiple model estimation problems, the goal of learning is to separate available data into several (disjoint) subsets, and at the same time estimate unknown models corresponding to each subset of data. This project describes several useful multiple model formulations, such as multiple model classification, multiple model regression, and multiple model clustering, and several real-life application settings where multiple model formulation approach can be naturally applied. 
We also describe a class of constructive learning algorithms for multiple model estimation. The proposed model estimation strategy assumes that the majority of available data is generated by a single model; hence we use robust methodology to estimate this (major) model. We use Support Vector Machine (SVM) based algorithm for robust model estimation. We developed SVM-based algorithms for multiple model regression and multiple model classification. Empirical comparisons performed using several simulated and real-life data sets indicate superior performance of the proposed learning algorithms. 
Finally, this thesis presents new methodology for analytic setting of hyper-parameters for SVM regression. This is important for practical applications of SVM regression in general, and for multiple model regression estimation, in particular.
Critique of Podiatric biomechanics by William Eric Lee, DPM. (2001)

This critique of Dr Lee's article is an attempt to clarify some misinterpretations and accreditations concerning his description of Dr Merton Root's work in biomechanics. The criticisms are based on personal discussion with most of the other mentioned authors and their teachings. Lee has been involved with the subject matter for 45 years and has had the benefit of practicing biomechanics since its beginning.
A role for preprophase bands of microtubules in maturation of new cell walls, and a general proposal on the function of preprophase band sites in cell division in higher plants (1990)

ABSTRACT Time-lapse video microscopy of dividing Tradescantia stamen hair cells that are undergoing cytokinesis has revealed that the maturation of the new cell wall is aided by factors at the site where the preprophase band of microtubules forms before mitosis. The wall changes from being fluid and wrinkled before it is inserted into the parental wall at the end of cytokinesis, to being stiff and flat by about 20 min after the time of attachment. This change occurs only if the new wall is inserted at the site formerly occupied by the preprophase band. The cell plate does not flatten when it is caused to insert elsewhere by drug treatments or by centrifugal displacement. If insertion at the correct site is delayed locally by centrifugation against the direction of expansion of the cell plate, then flattening is delayed at the same locality. In combination with a number of points from the literature of plant cell division, some of them very long-standing, our observations lead to a general proposal regarding the nature of the preprophase band site, its mode of action and timing of its operations, and how its role in spatial regulation of histogenesis is achieved.