gebhart/patrepeval huggingface dataset:
Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis (2013)

Amyotrophic lateral sclerosis is heterogeneous with high variability in the speed of progression even in cases with a defined genetic cause such as superoxide dismutase 1 (SOD1) mutations. We reported that SOD1(G93A) mice on distinct genetic backgrounds (C57 and 129Sv) show consistent phenotypic differences in speed of disease progression and life-span that are not explained by differences in human SOD1 transgene copy number or the burden of mutant SOD1 protein within the nervous system. We aimed to compare the gene expression profiles of motor neurons from these two SOD1(G93A) mouse strains to discover the molecular mechanisms contributing to the distinct phenotypes and to identify factors underlying fast and slow disease progression. Lumbar spinal motor neurons from the two SOD1(G93A) mouse strains were isolated by laser capture microdissection and transcriptome analysis was conducted at four stages of disease. We identified marked differences in the motor neuron transcriptome between the two mice strains at disease onset, with a dramatic reduction of gene expression in the rapidly progressive (129Sv-SOD1(G93A)) compared with the slowly progressing mutant SOD1 mice (C57-SOD1(G93A)) (1276 versus 346; Q-value ≤ 0.01). Gene ontology pathway analysis of the transcriptional profile from 129Sv-SOD1(G93A) mice showed marked downregulation of specific pathways involved in mitochondrial function, as well as predicted deficiencies in protein degradation and axonal transport mechanisms. In contrast, the transcriptional profile from C57-SOD1(G93A) mice with the more benign disease course, revealed strong gene enrichment relating to immune system processes compared with 129Sv-SOD1(G93A) mice. Motor neurons from the more benign mutant strain demonstrated striking complement activation, over-expressing genes normally involved in immune cell function. We validated through immunohistochemistry increased expression of the C3 complement subunit and major histocompatibility complex I within motor neurons. In addition, we demonstrated that motor neurons from the slowly progressing mice activate a series of genes with neuroprotective properties such as angiogenin and the nuclear factor (erythroid-derived 2)-like 2 transcriptional regulator. In contrast, the faster progressing mice show dramatically reduced expression at disease onset of cell pathways involved in neuroprotection. This study highlights a set of key gene and molecular pathway indices of fast or slow disease progression which may prove useful in identifying potential disease modifiers responsible for the heterogeneity of human amyotrophic lateral sclerosis and which may represent valid therapeutic targets for ameliorating the disease course in humans.
Method for the calculation of effective pore size distribution in molecular sieve carbon. (1983)

A method for the calculation of effective pore size distribution from adsorption isotherms in molecular-sieve carbon is described. This method is more exact theoretically as well as practically than previously described methods. An average potential function has been determined inside the slit-like pores. With the help of this function the doubtful use of the Kelvin equation can be avoided at the scale of molecular dimensions. The method gives poor values for the larger pores but can be combined with the well-known Dollimore-Heal method at a pore size of 1.34 nm. Calculation is possible over a wide range of pore sizes. The calculation is shown through two examples from N2 isotherms at 77.4K. The model can be extended to other pore shapes as well as to other adsorbent-adsorbate pairs.
Clinical and Biological Effects of an Agonist Anti-CD40 Antibody: A Cancer Research UK Phase I Study (2015)

ChiLob7/4 can activate B and NK cells at doses that can be administered safely, and should be tested in combination with other antibodies and chemotherapy agents.
Phase I Trial of TGF-β2 Antisense GM-CSF Gene-Modified Autologous Tumor Cell (TAG) Vaccine (2011)

On the basis of safety and clinical and immunologic results, further evaluation of bifunctional vaccines is warranted.
Characterization of SIS1, a Saccharomyces cerevisiae homologue of bacterial dnaJ proteins. (1991)

The Saccharomyces cerevisiae SIS1 gene was identified as a high copy number suppressor of the slow growth phenotype of strains containing mutations in the SIT4 gene, which encodes a predicted serine/threonine protein phosphatase. The SIS1 protein is similar to bacterial dnaJ proteins in the amino-terminal third and carboxyl-terminal third of the proteins. In contrast, the middle third of SIS1 is not similar to dnaJ proteins. This region of SIS1 contains a glycine/methionine-rich region which, along with more amino-terminal sequences, is required for SIS1 to associate with a protein of apparent molecular mass of 40 kD. The SIS1 gene is essential. Strains limited for the SIS1 protein accumulate cells that appear blocked for migration of the nucleus from the mother cell into the daughter cell. In addition, many of the cells become very large and contain a large vacuole. The SIS1 protein is localized throughout the cell but is more concentrated at the nucleus. About one-fourth of the SIS1 protein is released from a nuclear fraction upon treatment with RNase. We also show that overexpression of YDJ1, another yeast protein with similarity to bacterial dnaJ proteins, can not substitute for SIS1.
Bias detection and correction in RNA-Sequencing data (2011)

Our method identifies and corrects different sources of biases in gene-level expression measures from RNA-Seq data, and provides more accurate estimates of gene expression levels from RNA-Seq. This method should prove useful in meta-analysis of gene expression levels using different platforms or experimental protocols.
Tumor Cells Circulate in the Peripheral Blood of All Major Carcinomas but not in Healthy Subjects or Patients With Nonmalignant Diseases (2004)

The CellSearch system can be standardized across multiple laboratories and may be used to determine the clinical utility of CTCs. CTCs are extremely rare in healthy subjects and patients with nonmalignant diseases but present in various metastatic carcinomas with a wide range of frequencies.
Interleukin-18: biological properties and clinical implications. (2000)

IL-18, originally identified as interferon-gamma inducing factor (IGIF), is related to the IL-1 family in terms of its structure, processing, receptor, signal transduction pathway and pro-inflammatory properties. IL-18 is also functionally related to IL-12, as it induces the production of Th1 cytokines and participates in cell-mediated immune cytotoxicity. This review summarizes the recent advances in the understanding of IL-18 structure, processing, receptor expression and immunoregulatory functions, and focuses on the role of IL-18 modulation in tumours, infections, and autoimmune and inflammatory diseases.
Bivalve Mollusk Assemblage of Bed III, Olduvai Gorge, Tanzania (2014)

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Angiogenesis and Mineralization During Distraction Osteogenesis (2002)

Distraction osteogenesis is currently a standard method of bone lengthening. It is a viable method for the treatment of short extremities as well as extensive bone defects, because large amounts of bone can be regenerated in the distraction gap. Mechanical stimulation by distraction induces biological responses of skeletal regeneration that is accomplished by a cascade of biologic processes that may include differentiation of pluripotential tissue, angiogenesis, mineralization, and remodeling. There are complex interactions between bone-forming osteoblasts and other cells present within the bone microenvironment, particularly vascular endothelial cells that may be pivotal members of a complex interactive communication network in bone. Regenerate bone forms by three modes of ossification, which include intramembranous, enchondral, and transchondroid ossifications, although intramembraneous bone formation is the predominant mechanism of ossification. In this review we discussed the coupling between angiogenesis and mineralization, the biological and mechanical factors affecting them, the cellular and molecular events occurring during distraction osteogenesis, and the emerging modalities to accelerate regenerate bone healing and remodeling.
Efficacy and Safety of Technosphere Inhaled Insulin Compared With Technosphere Powder Placebo in Insulin-Naive Type 2 Diabetes Suboptimally Controlled With Oral Agents (2008)

Technosphere insulin was well tolerated and demonstrated significant improvement in glycemic control with clinically meaningful reductions in A1C levels and postprandial glucose concentrations after 12 weeks of treatment.
Variational-Inference-Based Data Detection for OFDM Systems With Imperfect Channel Estimation (2012)

This paper studies the problem of joint estimation of data and channels for orthogonal frequency-division multiplexing (OFDM) systems using variational inference. The proposed methods are used to combat imperfect channel estimation at the receiver since it can degrade system performance seriously. The proposed methods simplify the maximum a posteriori (MAP) scheme based on the theory of variational inference and formulate an optimization problem using variational free energy. The channel state information (CSI) and data are dealt with jointly and iteratively. The proposed schemes offer a variety of solutions for getting soft information when turbo equalization is implemented for coded systems. The effectiveness of the new approach is demonstrated by Monte Carlo simulations.
Macromolecular Electronic Device (1994)

Abstract A thin-film transistor (TFT) with high carrier mobility has been fabricated using poly(2,5-thienylenevinylene)(PTV) as semiconductor. The carrier mobility has been obtained to be 0.22cm2/Vsec, which is in the same level as that of amorphous silicon TFT. It has been indicated that the enlargement of the π-conjugation length is crucial for the improvement of the carrier mobility. It has been also demonstrated that the molecular orientation is another important factor in terms of the device characteristics.
Nano electrospray combined with a quadrupole ion trap for the analysis of peptides and protein digests (1996)

A nano electrospray (NanoES)/ion trap combination was developed to take advantage of the long spraying time of the NanoES source (Wilm, M. S., Mann, M. Int. J. Mass Spectrom. Ion Processes 1994, 136, 167-180) for extensive experiments on the ion trap. The low flow rate associated with the NanoES allows for optimization of experimental conditions and data acquisition for more than 30 min with 1 µL of solution. Thus, even time-consuming experiments, such as multiple fragmentation steps or the sequencing of many components in a mixture, can be performed with very small volumes of sample. Stored waveform inverse Fourier transformation (SWIFT) signals were used during the injection period to accumulate ions of low intensity and to improve the dynamic range of the quadrupole ion trap. To sequence peptides, a combination of nozzle-skimmer fragmentation, SWIFT accumulation of a single fragment to high intensity, and a second fragmentation step was employed to obtain complete sequence information. Unseparated peptide mixtures were infused and weak portions of the spectrum were enhanced by using the SWIFT method, followed by fragmentation of various accumulated peptide ions.
Ölümle Sonuçlanan Kadın Hastalıkları ve Doğum Olgularında Tıbbi Uygulama Hatası İddialarının Değerlendirilmesi (2020)

Amaç: Kadın Hastalıkları ve Doğum alanında ölüm gerçekleşmiş tıbbi uygulama hatası iddiası olgularının özellikleri ve adli tıbbi boyutu literatür eşliğinde değerlendirilerek, sağlık çalışanlarının ve kurumların tıbbi uygulama hatalarının ve uygulama nedeniyle yöneltilebilecek iddiaların azaltılması amaçlanmaktadır. Gereç ve Yöntem: 2012 – 2013 yıllarında Adli Tıp Kurumu (ATK) tarafından görüş bildirilmiş kadın hastalıkları ve doğum alanındaki sağlık görevlileri hakkında tıbbi uygulama hata iddiaları bulunan 452 olgu retrospektif olarak incelendi. Bulgular: Bilirkişi görüşü istenilen 452 olgunun % 8’inde (n:38) tıbbi uygulama hatası olduğu tespit edilmiştir. Tıbbi uygulama hata iddialarının en yüksek oranla Doğu Anadolu Bölgesinden, en sık özel hastanelerden ve uzman doktorlara yönelik davalardan kaynaklandığı gözlenmiştir. 35 yaş üzeri gebeliklerde maternal ölüm oranı, 35 yaş altı gebeliklere oranla anlamlı derecede yüksek bulunmuştur (p&amp;lt;0,001). Olguların en sık sezaryen doğum yaptığı (n:241, % 58,7) tespit edilmiş olup, normal doğum yapan olgulardaki tıbbi uygulama hatası varlığı, sezaryen doğum olgularındaki tıbbi uygulama hatası varlığından anlamlı derecede yüksek bulunmuştur (p&amp;lt;0,05). Hem jinekoloji olgularında, hem de maternal ölüm olgularında uterus atonisi en sık ölüm sebebi olurken, klinik tanı ile ATK tarafından belirlenen ölüm sebebi arasındaki ilişki değerlendirildiğinde; hem jinekoloji olguları, hem obstetrik olgular için uyumluluk oranının yüksek olduğu saptanmıştır (%58 -%61). Olgularda hem şikâyet, hem de tıbbi uygulama hatası nedeni olarak en sık özen eksikliği olduğu saptanmıştır. Sonuç: Tıbbi uygulama hata iddiası olgularında her olgunun kendi dinamikleriyle değerlendirilmesi gerekmektedir. Tıbbi uygulamaların kayıtlarının eksiksiz tutulmasının ve hasta hekim iletişiminin en doğru şekilde sağlanmasının tıbbi uygulama hatasını ve iddialarını azaltabileceği düşünülmektedir.
Inhibition of neuroblastoma cell growth by TREX1-mutated human lymphocytes (2012)

T lymphocytes play a major role in counteracting cancer occurrence and development. Immune therapies against cancer are focused on eliciting a cytotoxic T cell response. This anticancer activity is related to a variety of mechanisms including the activation of cytokines and proapoptotic mediators. Interferon α is an established inhibitor of cancer cell growth. A clinical situation involving the coexistence of high interferon α levels and lymphocyte activation is the Aicardi-Goutières syndrome, a progressive encephalopathy arising usually during the first year of life characterized by intracranial basal ganglia calcifications, leukodystrophy and microcephaly. Aicardi-Goutières syndrome 1 mutation silences the TREX1 gene, a major endogenous nuclease. The in vitro study presented herein evaluates the efficacy of the TREX1 mutation in potentiating the anticancer properties of T cells. A TREX1-mutated lymphocyte cell line was derived from an Aicardi-Goutières syndrome patient and co-cultured with neuroblastoma cells and vascular endothelial cells in the presence of interferon α. TREX1-mutated lymphocytes exerted marked inhibitory action on neuroblastoma cell growth. Cathepsin D was recognized by qPCR as the main mediator produced by TREX1-mutated lymphocytes involved in the inhibition of neuroblastoma cell growth. These effects were enhanced in the presence of interferon α. Similar inhibitory effects in cell growth were exerted by TREX1-mutated lymphocytes towards vascular endothelial cell angiogenesis as evaluated on Matrigel. The results obtained provide evidence that mutations of the TREX1 gene increase the capability of T-lymphocytes to inhibit growth of neoplastic neuronal cells and related angiogenesis.
Application of Pharmacokinetics to Computed Tomography (1996)

The computer program TOPFIT appears useful for the optimization of time--density profiles in computed tomography. The number of further clinical studies with the objective of optimization could therefore possibly be reduced.
IFN-α Suppresses Activation of Nuclear Transcription Factors NF-κB and Activator Protein 1 and Potentiates TNF-Induced Apoptosis (2000)

We and others have reported that IFN-alpha potentiates the apoptotic effects of TNF through a mechanism that is not understood. Because the nuclear transcription factors NF-kappaB and AP-1 have recently been reported to mediate anti-apoptosis and cell survival, we hypothesized that IFN-alpha potentiates the cytotoxic effects of TNF by suppressing TNF-induced activation of NF-kappaB and AP-1. We tested this hypothesis by pretreating human Jurkat T cells with IFN-alpha, which blocked TNF-induced activation of NF-kappaB and AP-1 in a time- and dose-dependent manner as determined by EMSA. IFN-alpha blocked TNF-induced phosphorylation and degradation of the inhibitor subunit of NF-kappaB, and suppressed NF-kappaB and AP-1 activation induced by various other inflammatory stimuli. NF-kappaB-dependent reporter gene expression activated by TNF, TNFR1, TNF receptor-associated factor 2, and NF-kappaB-inducing kinase was also abrogated by IFN-alpha pretreatment. The suppression of NF-kappaB and AP-1 correlated with the potentiation of TNF-induced cytotoxicity and caspase activation. Overall our results suggest that IFN-alpha potentiates the apoptotic effects of TNF possibly by suppressing NF-kappaB and AP-1 activation.
In Vitro Antimicrobial Activity of Wall Teichoic Acid Biosynthesis Inhibitors against Staphylococcus aureus Isolates (2010)

Staphylococcus aureus is the leading cause of invasive and superficial human infections, is increasingly antibiotic resistant, and is therefore the target for the development of new antimicrobials. Compounds (1835F03 and targocil) were recently shown to function as bacteriostatic inhibitors of wall teichoic acid (WTA) biosynthesis in S. aureus. To assess the value of targeting WTA biosynthesis in human infection, it was therefore of interest to verify the involvement of WTA in bacterial binding to human corneal epithelial cells (HCECs) and to assess the activities of inhibitors of WTA biosynthesis against clinical isolates of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) from cases of human keratitis. The 1835F03 MIC(90)s were 8 μg/ml for MSSA keratitis isolates and >32 μg/ml for MRSA keratitis isolates. The MIC(90) for the analog of 1835F03, targocil, was 2 μg/ml for both MRSA and MSSA. Targocil exhibited little toxicity at concentrations near the MIC, with increased toxicity occurring at higher concentrations and with longer exposure times. Targocil activity was moderately sensitive to the presence of serum, but it inhibited extracellular and intracellular bacteria in the presence of HCECs better than vancomycin. Targocil-resistant strains exhibited a significantly reduced ability to adhere to HCECs.
Optimum bit allocation and decomposition for high quality audio coding (2002)

Current audio compression schemes are capable of reducing the per channel bit rate of high quality audio signals from 16 bits per sample to around 2-4 bits per sample. In these schemes, knowledge of psychoacoustics is utilised and a uniform or nonuniform frequency decomposition method is used. In this paper we derive the optimum bit allocation to achieve the highest perceptual quality under a fixed bit rate, for an arbitrarily decomposed, critically sampled, filter bank. The resultant optimum bit allocation gives rise to a shaped reconstruction noise floor approximately parallel to the masking threshold level. Perceptual coding gain is defined and should be maximized for an optimum decomposition performed by the filter bank. Optimum band splitting is discussed and it is pointed out that decomposition in the manner of critical band splitting does not lead to optimal performance.
The Cat: Diseases and Clinical Management (1994)

Volume I: The Clinical Foundations of Feline Practice. Nutrition. Behavior. Intoxication and Injury. Infectious Diseases. Parasitic Diseases. Immunology, Hematology and Oncology. The Cardiopulmonary System. Index. Volume II: The Digestive System. The Endocrine System. The Neuromuscular System. The Skeletal System. The Urinary System. The Reproductive System. The Skin. The Ears and the Eyes. Index.
Modeling and intelligent control design of car following behavior in real traffic flow (2010)

The control of car following is essential to its safety and its operational efficiency. For this purpose, this paper builds a linear, continuous and time-delay model of car following. And then, presents a controller based on an adaptive network fuzzy inference system (ANFIS) for the car-following collision avoidance system to adaptively control the speed of the vehicle. The relative distance and relative speed to the in front car are measured and are applied to the controller. The output acceleration or deceleration rate of the controller is based on the characteristics of the vehicles. The presented ANFIS controller can solve the problems of the oscillations for final distance between the leader vehicle (LV) and the follower vehicle (FV) and their relative speed. The designed ANFIS controller is linked to the car following model. The simulation results show that the ANFIS control design is more effective and can provide a safe, reasonable, and comfortable drive than real driver.
The role of the cell adhesion molecule uvomorulin in the formation and maintenance of the epithelial junctional complex. (1988)

The role of the epithelial adhesion molecule uvomorulin in the formation of the epithelial junctional complex in the Madin-Darby canine kidney (MDCK) cell line was investigated. Experiments were carried out to determine whether specific inhibition of uvomorulin function would interfere selectively with the formation, stability, or function of the apical zonula adherens (ZA) and zonula occludens (ZO), or whether it would interfere with all forms of intercellular contact including the desmosomes. The effects of blocking antibodies and Fab fragments to uvomorulin on the formation of the junctional complex was examined with a Ca2+ switch assay for de novo junction assembly. The formation of the ZO, the ZA, and the desmosomes was assayed by fluorescence staining with an antibody to the tight junction-specific protein ZO-1, with rhodamine-phalloidin for ZA-associated actin filaments, and with an anti-desmoplakin antibody, respectively. Under different conditions and times of antibody treatment the extent of inhibition of the formation of each of the junctional elements was very similar. The ability of the cells to eventually overcome the inhibitory effect of the antibodies and form junctions correlated with the reappearance of uvomorulin at the regions of cell-cell contact. Therefore uvomorulin seems to mediate an early adhesion event between epithelial cells that is a prerequisite for the assembly of all elements of the junctional complex. In contrast, the transepithelial electrical resistance of confluent, well-established monolayers of MDCK cells grown on filters was not greatly affected by treatment with the various antibodies or Fab fragments. A small transient decrease in resistance observed with the polyclonal alpha-uvomorulin IgG may be due to a more subtle modulation of the junctional complex.