gebhart/patrepeval huggingface dataset:
Mastering Perl for Bioinformatics (2003)

Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis. Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics. The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: Gene findingString alignmentMethods of data storage and retrieval (SML and databases)Modeling of networks (graphs and Petri nets)Graphics (Tk)ParallelizationInterfacing with other programming languagesStatistics (PDL)Protein structure determinationBiological models of computation (DNA Computers) Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.
Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma (2017)

We previously reported an extremely rare case of follicular dendritic cell sarcoma (FDCS) presented as a thyroid mass. Given the rarity of this disease, there are no personalized and molecularly targeted treatment options due to the lack of knowledge in the genomic makeup of the tumor. A 44-year-old white woman was diagnosed with an extranodal FDCS in thyroid. The patient underwent a total thyroidectomy, central compartment dissection, parathyroid re-implantation, and adjuvant radiation therapy. Tumor DNA sequencing of 236 genes by FoundationOne panel found truncating mutations in PTEN and missense mutations in RET and TP53. However, patient-matched germline DNA was not sequenced which is critical for identification of true somatic mutations. Furthermore, the FoundationOne panel doesn't measure genomic rearrangements which have been shown to be abundant in sarcomas and are associated with sarcoma tumorigenesis and progression. In the current study, we carried out comprehensive genomic sequencing of the tumor, adjacent normal tissues, and patient-matched blood, in an effort to understand the genomic makeup of this rare extranodal FDCS and to identify potential therapeutic targets. Eighty-one somatic point mutations were identified in tumor but not in adjacent normal tissues or blood. A clonal truncating mutation in the <i>CLTCL1</i> gene, which stabilizes the mitotic spindle, was likely a driver mutation of tumorigenesis and could explain the extensive copy number aberrations (CNAs) and genomic rearrangements in the tumor including a chr15/chr17 local chromothripsis resulted in 6 expressed fusion genes. The fusion gene HDGFRP3→SHC4 led to a 200-fold increase in the expression of oncogene SHC4 which is a potential target of the commercial drug Dasatinib. Missense mutations in <i>ATM</i> and splice-site mutation in <i>VEGFR1</i> were also detected in addition to the TP53 missense mutation reported by FoundationOne.
A comparison of balloon injury models of endovascular lesions in rat arteries (2002)

BI resulted in: (1.) a decrease in LD in CCA due to IH, (2.) a decrease in LD in CIA due to IH and CVR, (3.) no change in LD in AA, (4.) Comparable IH development in all arteries, (5.) CCA has no vasa vasorum compared to CIA and AA, (6.) The CIA model combines good access for 2 F endovascular catheters with a decrease in LD due to IH and CVR after BI.
Stimulation of mucosal immune response following oral administration of enterotoxigenic Escherichia coli fimbriae (CFA/I) entrapped in liposomes in conjunction with inactivated whole-cell Vibrio cholerae vaccine. (2002)

In this study, we have searched for an effective mucosal vaccine. An oral enterotoxigenic E. coli vaccine containing colonization factor antigen (CFA/I) associated with inactivated whole-cell V. cholerae vaccine (WCV) has been tested for safety and immunogenicity in animals. Five groups of animals were used. The results showed the following: (a) vaccine containing CFA/I antigen entrapped in liposomes and associated with WCV (batch C) had increased titers of specific antibodies to CFA/I antigen in 15 to 18 (83.3%) animals; (b) specific Peyer's patches (PP), lymph nodes (LN) and spleen (SPL) lymphocytes proliferation was detected following in vitro restimulation with CFA/I antigen or WCV. This response gradually increased to the highest value by the 35th postimmunization day. Moreover, lower PP, LN and spleen (SPL) proliferation was observed in rabbits receiving soluble CFA/I antigen (S-CFA/I) or free liposomes (F-L) alone; (c) adhesion of E. coli H10407 strain labelled with 3H-leucine in immunized and control animals revealed the following local effects: (i) protection of rabbit intestinal mucosa against virulent E. coli cells; (ii) inhibition of adhesion of ETEC bacteria to intestinal mucosa and (iii) significantly faster release of E. coli H 10407 strain labelled with 3H-leucine from the intestinal tract of immunized animals. The histopathological and electron microscope findings confirmed the above results. The experimental results point out an efficient protection against infection with E. coli strains (ETEC), after mucosal vaccination with CFA/I antigen entrapped in liposomes associated with inactivated whole-cell Vibrio cholerae as immunological adjuvant.
Alkyl-bis(imidazolium) salts: a new amphiphile platform that forms thermotropic and non-aqueous lyotropic bicontinuous cubic phases (2013)

New ionic amphiphiles with a hexyl-bridged bis(imidazolium) headgroup; Br(-), BF4(-), or Tf2N(-) anions; and a long n-alkyl tail can form thermotropic bicontinuous cubic liquid crystal phases in neat form and/or lyotropic bicontinuous cubic phases with several non-aqueous solvents or water.
Troglitazone: Review and Assessment of Its Role in the Treatment of Patients with Impaired Glucose Tolerance and Diabetes Mellitus (1998)

Troglitazone appears to be a safe, effective, and useful new agent in the treatment of insulin-requiring type 2 diabetes mellitus patients, although its HbA1C-lowering effects have been minimal in short-term trials, and its insulin dosage-reduction activity remains unclear. The Food and Drug Administration has also approved its use as monotherapy and in combination with sulfonylureas for patients with type 2 diabetes. It may have use in the treatment of patients with impaired glucose tolerance, but more clinical experience is needed before definitive conclusions can be made. The role of troglitazone therapy in diabetes mellitus and impaired glucose intolerance will continue to evolve as the results of studies and our clinical experience with this agent become available.
Analysis of the Decision Rules in Decision Tables (1963)

Decision tables, a framework for describing a set of related decision rules, can improve the communication and documentation achievable by previous techniques such a charting and narrative descriptions of data processing problems, particularly those containing many complex decision rules. In addition, decision tables offer system analysts the potential to eliminate inconsistencies and redundancies in each set of specified decision rules and to produce computer programs that are efficient in the use of computer storage and computer running time. Decision tables also enable the system analyst to determine if he has considered all of the possible decision rules that can be formed from a particular set of conditions. This Memo randum develops for decision tables a theoretical structure that serves as the foundation for achieving these benefits. As background for this development, the author describes a basic structure of decision tables. The theorems developed in this paper provide a basis for system analysts and programmers to verify the logic of their analysis.
Enhanced microfiltration devices configured with hydrodynamic trapping and a rain drop bypass filtering architecture for microbial cells detection (2008)

Ultra-fine (<1 microm) microfilters are required to effectively trap microbial cells. We designed microfilters featuring a rain drop bypass architecture, which significantly reduces the likelihood of clogging at the cost of limited cell loss. The new rain drop bypass architecture configuration has a substantially lower pressure drop and allows a better efficiency in trapping protozoan cells (Cryptosporidium parvum and Giardia lamblia) in comparison to our previous generation of a microfilter device. A modified version displaying sub-micron filter gaps was adapted to trap and detect bacterial cells (Escherichia coli), through a method of cells labeling, which aims to amplify the fluorescence signal emission and therefore the sensitivity of detection.
Purification and characterization of aromatic acid reductase from Nocardia asteroides JCM 3016. (1991)

Aromatic acid reductase (aryl-aldehyde dehydrogenase, EC 1.2.1.30) was purified to electrophoretic homogeneity from Nocardia asteroides JCM 3016. The enzyme was a monomeric protein with a molecular weight of 152, 000. The enzyme absolutely required ATP, NADPH, and MgCl2 for the reduction of benzoate to benzaldehyde. In the overall reaction, benzaldehyde, AMP, and NADP+ were stoichiometrically formed from benzoate, ATP and NADPH, respectively. The purified enzyme catalyzed the reduction of benzoyl adenosine 5'-monophosphate (bzAMP), which is the intermediate formed from benzoate and ATP. The temperature dependence of the benzoate- and bzAMP-reducing activities agreed exactly, and the same Km for NADPH was obtained by the steady state kinetics of both reactions. These results suggest that the overall reduction of benzoate proceeds via bzAMP, and that the ATP-dependent adenylation of benzoate and the reduction of bzAMP are catalyzed by one enzyme. The enzyme was fairly specific for meta-substituted benzoates.
Investigation of the formation of undercut during the fabrication of silicon microchannels by electrochemical etching (2008)

Silicon microchannel plates have been explored intensively for numerous applications especially for weak light detection and night vision. The electrochemical etching in hydrofluoric acid-based solutions is known as a technique for porous silicon formation. This paper presents a new process for the formation of microchannel structure and the separation of the Si MCP from p-type starting substrates by a single-step electrochemical etching in HF-based electrolytes. High aspect ratio microchannels are fabricated by electrochemical etching and the conditions under which the undercut occurs are investigated. The formation of the undercut is found to be primarily determined by both current density and HF concentration, which determine the MCP structure thickness as well.
Large-scale temporal gene expression mapping of central nervous system development (1998)

We used reverse transcription-coupled PCR to produce a high-resolution temporal map of fluctuations in mRNA expression of 112 genes during rat central nervous system development, focusing on the cervical spinal cord. The data provide a temporal gene expression "fingerprint" of spinal cord development based on major families of inter- and intracellular signaling genes. By using distance matrices for the pair-wise comparison of these 112 temporal gene expression patterns as the basis for a cluster analysis, we found five basic "waves" of expression that characterize distinct phases of development. The results suggest functional relationships among the genes fluctuating in parallel. We found that genes belonging to distinct functional classes and gene families clearly map to particular expression profiles. The concepts and data analysis discussed herein may be useful in objectively identifying coherent patterns and sequences of events in the complex genetic signaling network of development. Functional genomics approaches such as this may have applications in the elucidation of complex developmental and degenerative disorders.
Identification of a truncated form of the CC chemokine CK beta-8 demonstrating greatly enhanced biological activity. (1998)

A new CC chemokine, designated CKbeta-8 or myeloid progenitor inhibitor factor-1, was recently identified in a large scale sequencing effort and was cloned from a human aortic endothelial library. CKbeta-8 cDNA encodes a signal sequence of 21 amino acids, followed by a 99-amino acid predicted mature form. CKbeta-8 was expressed and purified from a baculovirus insect cell expression system, which resulted in the identification of different N-terminal variants of the secreted chemokine. The three major forms (containing amino acids 1-99, 24-99, and 25-99 of the secreted chemokine) showed a large variation in potency. CKbeta-8 activated both monocytes and eosinophils to mobilize intracellular calcium; however, the shortest form of CKbeta-8 (25-99) was >2 orders of magnitude more potent than the longest form. Cross-desensitization experiments in both monocytes and eosinophils suggested that the CCR1 receptor was probably the predominant receptor that mediates this chemokine's physiologic response. However, incomplete desensitization was encountered in both cell systems, suggesting involvement of an additional receptor(s). Interestingly, the short form of CKbeta-8 was the most potent chemotactic chemokine that we have ever evaluated in the monocyte system (EC50 = 54 pM). However, in contrast to its action on monocytes, CKbeta-8 was a very poor chemotactic factor for eosinophils.
A computationally efficient hybrid of joint detection and successive interference cancellation (2002)

We propose a multiuser detection (MUD) receiver that adaptively combines varying degrees of joint detection (JD) and successive interference cancellation (SIC). allowing a trade-off between complexity and performance. It arranges users of roughly similar power into groups and performs a group-wise JD to mitigate intersymbol interference (ISI) and multiple access interference (MAI) within each group. It removes MAI between groups via SIC. Analysis indicates that a complexity which is 60% to 30% that of JD is achievable while the performance is comparable to that of JD. Key applications include burst mode wideband-CDMA systems such as the 3rd generation time division duplex system.
Modulation of the Heparanase-inhibiting Activity of Heparin through Selective Desulfation, Graded N-Acetylation, and Glycol Splitting (2005)

Heparanase is an endo-beta-glucuronidase that cleaves heparan sulfate (HS) chains of heparan sulfate proteoglycans on cell surfaces and in the extracellular matrix (ECM). Heparanase, overexpressed by most cancer cells, facilitates extravasation of blood-borne tumor cells and causes release of growth factors sequestered by HS chains, thus accelerating tumor growth and metastasis. Inhibition of heparanase with HS mimics is a promising target for a novel strategy in cancer therapy. In this study, in vitro inhibition of recombinant heparanase was determined for heparin derivatives differing in degrees of 2-O- and 6-O-sulfation, N-acetylation, and glycol splitting of nonsulfated uronic acid residues. The contemporaneous presence of sulfate groups at O-2 of IdoA and at O-6 of GlcN was found to be non-essential for effective inhibition of heparanase activity provided that one of the two positions retains a high degree of sulfation. N-Desulfation/ N-acetylation involved a marked decrease in the inhibitory activity for degrees of N-acetylation higher than 50%, suggesting that at least one NSO3 group per disaccharide unit is involved in interaction with the enzyme. On the other hand, glycol splitting of preexisting or of both preexisting and chemically generated nonsulfated uronic acids dramatically increased the heparanase-inhibiting activity irrespective of the degree of N-acetylation. Indeed N-acetylated heparins in their glycol-split forms inhibited heparanase as effectively as the corresponding N-sulfated derivatives. Whereas heparin and N-acetylheparins containing unmodified D-glucuronic acid residues inhibited heparanase by acting, at least in part, as substrates, their glycol-split derivatives were no more susceptible to cleavage by heparanase. Glycol-split N-acetylheparins did not release basic fibroblast growth factor from ECM and failed to stimulate its mitogenic activity. The combination of high inhibition of heparanase and low release/potentiation of ECM-bound growth factor indicates that N-acetylated, glycol-split heparins are potential antiangiogenic and antimetastatic agents that are more effective than their counterparts with unmodified backbones.
Treatment of the Irritable Bowel Syndrome with Bentyl® (Dicyclomine Hydrochloride) (1981)

The effectiveness of Bentyl (dicyclomine hydrochloride) 40 mg 4 times daily was evaluated in an ambulatory population with recent irritable bowel syndrome (IBS). During the 2-week double-blind study, the effects of dicyclomine hydrochloride compared to placebo were assesed by: 1) physicians' global evaluation of treatment, 2) patients' self-evaluation of treatment, and 3) patients' evaluation of duration of abdominal pain. It was concluded that over a 2-week period dicyclomine hydrochloride 40 mg 4 times a day is superior to placebo in improving the overall condition of the patient, decreasing abdominal pain, decreasing abdominal tenderness, and improving bowel habits. The majority of adverse effects reported were related to the anti-cholinergic activity of the drug.
Exosome-Mediated Transfer of miR-133b from Multipotent Mesenchymal Stromal Cells to Neural Cells Contributes to Neurite Outgrowth (2012)

Multipotent mesenchymal stromal cells (MSCs) have potential therapeutic benefit for the treatment of neurological diseases and injury. MSCs interact with and alter brain parenchymal cells by direct cell-cell communication and/or by indirect secretion of factors and thereby promote functional recovery. In this study, we found that MSC treatment of rats subjected to middle cerebral artery occlusion (MCAo) significantly increased microRNA 133b (miR-133b) level in the ipsilateral hemisphere. In vitro, miR-133b levels in MSCs and in their exosomes increased after MSCs were exposed to ipsilateral ischemic tissue extracts from rats subjected to MCAo. miR-133b levels were also increased in primary cultured neurons and astrocytes treated with the exosome-enriched fractions released from these MSCs. Knockdown of miR-133b in MSCs confirmed that the increased miR-133b level in astrocytes is attributed to their transfer from MSCs. Further verification of this exosome-mediated intercellular communication was performed using a cel-miR-67 luciferase reporter system and an MSC-astrocyte coculture model. Cel-miR-67 in MSCs was transferred to astrocytes via exosomes between 50 and 100 nm in diameter. Our data suggest that the cel-miR-67 released from MSCs was primarily contained in exosomes. A gap junction intercellular communication inhibitor arrested the exosomal microRNA communication by inhibiting exosome release. Cultured neurons treated with exosome-enriched fractions from MSCs exposed to 72 hours post-MCAo brain extracts significantly increased the neurite branch number and total neurite length. This study provides the first demonstration that MSCs communicate with brain parenchymal cells and may regulate neurite outgrowth by transfer of miR-133b to neural cells via exosomes.
Thermal isolation of microchip reaction chambers for rapid non-contact DNA amplification (2007)

This paper describes further optimization of a non-contact, infrared-mediated system for microchip DNA amplification via the polymerase chain reaction (PCR). The optimization is focused on heat transfer modeling and subsequent fabrication of thermally isolated reaction chambers in glass devices that are uniquely compatible with non-contact thermal control. With a thermal conductivity approximately an order of magnitude higher than many plastics, glass is not the obvious substrate of choice for rapid thermal cycling in microfluidic chambers, yet it is preferable in terms of optical clarity, solvent compatibility and chemical inertness. Based on predictions of a lumped capacity heat transfer analysis, it is shown here that post-bonding, patterned etching of surrounding glass from microfluidic reaction chambers provides enhancements as high as 3.6- and 7.5-fold in cooling and heating rates, respectively, over control devices with the same chamber designs. These devices are then proven functional for rapid DNA amplification via PCR, in which 25 thermal cycles are completed in only 5 min in thermally isolated PCR chambers of 270 nL volume, representing the fastest static PCR in glass devices reported to date. Amplification of the 500-base pair fragment of λ-DNA was confirmed by capillary gel electrophoresis. In addition to rapid temperature control, the fabrication scheme presented, which is compatible with standard photolithography and wet etching techniques, provides a simple alternative for general thermal management in glass microfluidic devices without metallization.
An overview of the Etherphone system and its applications (2003)

The Etherphone system has been developed to explore methods for extending existing multimedia office environments with the facilities needed to handle the transmission, storage, and manipulation of voice. Based on a hardware architecture that uses microprocessor-controlled telephones to transmit voice over an Ethernet that also supports a voice file server and a voice synthesis server, this system has been used for applications such as directory-based call placement, call logging, call filtering, and automatic call forwarding. Voice mail, voice annotation of multimedia documents, voice editing using standard text-editing techniques, and applications of synthetic voice use the Etherphones for voice transmission. Recent work has focused on the creation of a comprehensive voice system architecture, both to specify programming interfaces for custom uses of voice, and to specify the roles of different system components, so that equipment from multiple vendors could be integrated to provide sophisticated voice services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>