gebhart/patrepeval huggingface dataset:
Treatment of C-stage and E-stage effluents from a bleach plant using a ceramic membrane (1988)

C-stage effluent, E-stage effluent and a total effluent (C-stage and E-stage effluent mixed in proportion to the volumes of the effluents at the mill) have been treated with a ceramic microfilter membrane. The flux of the total effluent was considerably lower than of the separate effluents. The fluxes of the E-stage and C-stage effluents were 550 and 1,300 l/m2h, respectively, while the flux of the total effluent was only 150 l/m2h. The low filtration capacity is thought to be caused by adsorption of substances onto the membrane. The influence of pH on the filtration capacity of C- and E-stage effluent was clearly demonstrated.
Multi-strategy and multi-algorithm cochlear prostheses. (2000)

Over the past few years, two generations of cochlear implants have been designed and tested by our group. Since the beginning, our goal was to design a system that is completely transparent to sound processing algorithms and stimulation strategies. The first generation micro-stimulator has eight completely independent channels and the second generation one has sixteen. Each of them is mounted on a thick film hybrid circuit together with necessary interfacing components. The electronic circuits are housed in a hermetically sealed titanium case. They are able to deliver monopolar, bipolar, simultaneous or non-simultaneous stimuli on all of their channels. Their electrodes are addressable with all possible combinations. The eight-channel stimulator has already been successfully implanted on volunteer profoundly deaf patients, validating our concepts and our approaches. The second one is endowed with more flexibility and transparency to stimulation algorithms. It offers extended possibilities and more electrodes combinations. In a second version, this one has also been mounted on a thin film hybrid circuit making its size considerably reduced and allowing implanting it in other sites rather than on the temporal bone. The sound processor supporting these systems communicates with internal parts through an inductive link. It is built around a powerful DSP and can be programmed with more than one algorithm at a time. It has been already programmed with all the known strategies and some original ones such as the technique of vector quantization. The latter uses a dictionary of pre-stored stimulation patterns mapped to sound segments. As for programming the systems, this is accomplished by mean of specific user-friendly application software using a window driven completely graphical interface.
Engineering Escherichia coli into a Protein Delivery System for Mammalian Cells (2015)

Many Gram-negative pathogens encode type 3 secretion systems, sophisticated nanomachines that deliver proteins directly into the cytoplasm of mammalian cells. These systems present attractive opportunities for therapeutic protein delivery applications; however, their utility has been limited by their inherent pathogenicity. Here, we report the reengineering of a laboratory strain of Escherichia coli with a tunable type 3 secretion system that can efficiently deliver heterologous proteins into mammalian cells, thereby circumventing the need for virulence attenuation. We first introduced a 31 kB region of Shigella flexneri DNA that encodes all of the information needed to form the secretion nanomachine onto a plasmid that can be directly propagated within E. coli or integrated into the E. coli chromosome. To provide flexible control over type 3 secretion and protein delivery, we generated plasmids expressing master regulators of the type 3 system from either constitutive or inducible promoters. We then constructed a Gateway-compatible plasmid library of type 3 secretion sequences to enable rapid screening and identification of sequences that do not perturb function when fused to heterologous protein substrates and optimized their delivery into mammalian cells. Combining these elements, we found that coordinated expression of the type 3 secretion system and modified target protein substrates produces a nonpathogenic strain that expresses, secretes, and delivers heterologous proteins into mammalian cells. This reengineered system thus provides a highly flexible protein delivery platform with potential for future therapeutic applications.
Bidirectional excision in methyl-directed mismatch repair (1993)

Using electron microscopy and indirect end-labeling methods, we have examined excision tracts produced by the Escherichia coli methyl-directed mismatch repair system on a closed circular G-T heteroduplex that contains a single d(GATC) site. Despite differing polarities of the unmodified strand in the two hemimethylated derivatives of the heteroduplex, that portion of the unmethylated strand spanning the shorter path between the d(GATC) site and mismatch is targeted for excision in both cases. Mismatch-provoked excision occurring on both hemimethylated DNAs requires DNA helicase II, but exonuclease requirements for the reaction depend on heteroduplex orientation. When the d(GATC) sequence on the unmodified strand resides 3' to the mismatch as viewed along the shorter path, excision requires exonuclease I. Excision occurring on the alternate hemimethylated heteroduplex depends on the 5'--> 3' hydrolytic activity of exonuclease VII. Coupled with the previous demonstration that repair initiates via the mismatch-provoked, MutHLS-dependent incision of the unmethylated strand at a d(GATC) sequence (Au, K.G., Welsh, K., and Modrich, P. (1992) J. Biol. Chem. 267, 12142-12148), these findings indicate an excision mechanism in which helicase II displacement renders the incised strand sensitive to the appropriate single-strand exonuclease. Our data imply that hydrolysis commences at the d(GATC) site, proceeds to a point beyond the mismatch, and terminates at a number of discrete sites within a 100-nucleotide region just beyond this site. The extent of excision is therefore controlled by one or more components of the repair system.
Audio-visual content-based violent scene characterization (2002)

We present a novel technique to characterize and index violent scenes in general TV drama and movies. Our goal is to identify violent signatures and localize violent events within a movie to support "high-level" video indexing. In particular, we exploit multiple "audio-visual" signatures to create a perceptual relation for conceptually meaningful violent scene identification. Potential applications are automatic blocking of violence in movies watched by children, hiding violence using data hiding or information filtering and genre classification of digital video database.
SOCS1 is essential for regulatory T cell functions by preventing loss of Foxp3 expression as well as IFN-γ and IL-17A production (2011)

Regulatory T cells (T(reg) cells) maintain immune homeostasis by limiting inflammatory responses. SOCS1 (suppressor of cytokine signaling 1), a negative regulator of cytokine signaling, is necessary for the suppressor functions of T(reg) cells in vivo, yet detailed mechanisms remain to be clarified. We found that Socs1(-/-) T(reg) cells produced high levels of IFN-γ and rapidly lost Foxp3 when transferred into Rag2(-/-) mice or cultured in vitro, even though the CNS2 (conserved noncoding DNA sequence 2) in the Foxp3 enhancer region was fully demethylated. Socs1(-/-) T(reg) cells showed hyperactivation of STAT1 and STAT3. Because Foxp3 expression was stable and STAT1 activation was at normal levels in Ifnγ(-/-)Socs1(-/-) T(reg) cells, the restriction of IFN-γ-STAT1 signaling by SOCS1 is suggested to be necessary for stable Foxp3 expression. However, Ifnγ(-/-)Socs1(-/-) T(reg) cells had hyperactivated STAT3 and higher IL-17A (IL-17) production compared with Ifnγ(-/-)Socs1(+/+) T(reg) cells and could not suppress colitis induced by naive T cells in Rag2(-/-) mice. In vitro experiments suggested that cytokines produced by Socs1(-/-) T(reg) cells and Ifnγ(-/-)Socs1(-/-) T(reg) cells modulated antigen-presenting cells for preferential Th1 and Th17 induction, respectively. We propose that SOCS1 plays important roles in T(reg) cell integrity and function by maintaining Foxp3 expression and by suppressing IFN-γ and IL-17 production driven by STAT1 and STAT3, respectively.
Aberrant functional connectivity of dorsolateral prefrontal and cingulate networks in patients with major depression during working memory processing (2008)

These results complement and expand previous functional neuroimaging findings by demonstrating a dysconnectivity of dissociable prefrontal and cingulate regions in MDD patients. A disturbance of these dynamic networks is characterized by a simultaneously increased connectivity of the DLPFC during task-induced activation and increased connectivity of the ACC during task-induced deactivation.
SNP Genotyping: Technologies and Biomedical Applications (2007)

Single nucleotide polymorphisms (SNPs) are the most frequently occurring genetic variation in the human genome, with the total number of SNPs reported in public SNP databases currently exceeding 9 million. SNPs are important markers in many studies that link sequence variations to phenotypic changes; such studies are expected to advance the understanding of human physiology and elucidate the molecular bases of diseases. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis, yielding a large number of distinct approaches. This article presents a review of SNP genotyping techniques and examines their principles of genotype determination in terms of allele differentiation strategies and detection methods. Further, several current biomedical applications of SNP genotyping are discussed.
Bioengineered coagulation factor VIII enables long-term correction of murine hemophilia A following liver-directed adeno-associated viral vector delivery (2014)

Clinical data support the feasibility and safety of adeno-associated viral (AAV) vectors in gene therapy applications. Despite several clinical trials of AAV-based gene transfer for hemophilia B, a unique set of obstacles impede the development of a similar approach for hemophilia A. These include (i) the size of the factor VIII (fVIII) transgene, (ii) humoral immune responses to fVIII, (iii) inefficient biosynthesis of human fVIII, and (iv) AAV vector immunity. Through bioengineering approaches, a novel fVIII molecule, designated ET3, was developed and shown to improve biosynthetic efficiency 10- to 100-fold. In this study, the utility of ET3 was assessed in the context of liver-directed, AAV-mediated gene transfer into hemophilia A mice. Due to the large size of the expression cassette, AAV-ET3 genomes packaged into viral particles as partial genome fragments. Despite this potential limitation, a single peripheral vein administration of AAV-ET3 into immune-competent hemophilia A mice resulted in correction of the fVIII deficiency at lower vector doses than previously reported for similarly oversized AAV-fVIII vectors. Therefore, ET3 appears to improve vector potency and mitigate at least one of the critical barriers to AAV-based clinical gene therapy for hemophilia A.
Use of Dipmeter Data in Clastic Sedimentological Studies (1) (1990)

Resistivity curves from he eight measuring electrodes of Schlumberger's Stratigraphic High-Resolution Dipmeter Tool{TM} (SHDT) can be processed to give a detailed reservoir characteriation that includes electrofacies and sedimentary dip data. This conclusion is supported by evaluation of processed SHDT data compared with information from over 1,000 m (3,280 ft) of cores covering fluvial and eolian sedimentary environments. Based on three examples, we give general guidelines for processing of and noise removal from SHDT data to obtain satisfactory geological information. Foreset dips in sets as thin as 20 cm (8 in.) can be reliably calculated by using side-by-side processing options with a correlation interval of 10 cm (4 in.) and a step distance of 7.5 cm (3 in.). In many formations, spurious dip readings cause serious problems. These readings originate from irregularities in the formation or from processing artifacts, have no directional implication, and produce unsatisfactory signal-to-noise ratios. However, criteria have been defined to select relevant dips from such noisy data. Structural dips must be measured with a sufficient degree of confidence to accurately subtract them from sedimentary dips. Reliable data can be obtained by large-scale interval correlation, particularly when the interpretation is concentrated on suitable intervals (laminated shales and horizontally bedded heterolithic sequences). The SHDT tool also can provide detailed information on reservoir characteristics, particularly on small-scale heterogeneities that escape the resolution of conventional logs. Boreholewide resistivity displays from interpolation of SHDT traces enable the recognition of resistivity distribution patterns and may give a new scope to facies recognition from logs.
Cytokines as biochemical markers for knee osteoarthritis (2015)

Osteoarthritis (OA) is a debilitating degenerative joint disease particularly affecting weightbearing joints within the body, principally the hips and knees. Current radiographic techniques are insufficient to show biochemical changes within joint tissue which can occur many years before symptoms become apparent. The need for better diagnostic and prognostic tools is heightened with the prevalence of OA set to increase in aging and obese populations. As inflammation is increasingly being considered an important part of OAs pathophysiology, cytokines are being assessed as possible candidates for biochemical markers. Cytokines, both pro- and anti-inflammatory, as well as angiogenic and chemotactic, have in recent years been studied for relevant characteristics. Biochemical markers show promise in determination of the severity of disease in addition to monitoring of the efficacy and safety of disease-modifying OA drugs, with the potential to act as diagnostic and prognostic tools. Currently, the diagnostic power of interleukin (IL)-6 and the relationship to disease burden of IL-1β, IL-15, tumor necrosis factor-α, and vascular endothelial growth factor make these the best candidates for assessment. Grouping appropriate cytokine markers together and assessing them collectively alongside other bone and cartilage degradation products will yield a more statistically powerful tool in research and clinical applications, and additionally aid in distinguishing between OA and a number of other diseases in which cytokines are known to have an involvement. Further large scale studies are needed to assess the validity and efficacy of current biomarkers, and to discover other potential biomarker candidates.
The pituitary tumor transforming gene 1 (PTTG-1): An immunological target for multiple myeloma (2008)

We established PTTG-1's presence at both the transcriptional and protein levels. These data suggest that PTTG-1 is aberrantly expressed in multiple myeloma plasma cells, is highly immunogenic and is a suitable target for immunotherapy of multiple myeloma.
The Complete Primary Structure of Mouse α2 (IV) Collagen (1989)

We have determined the nucleotide and amino acid sequences of mouse alpha 2(IV) collagen which is 1707 amino acids long. The primary structure includes a putative 28-residue signal peptide and contains three distinct domains: 1) the 7 S domain (residues 29-171), which contains 5 cysteine and 8 lysine residues, is involved in the cross-linking and assembly of four collagen IV molecules; 2) the triple-helical domain (residues 172-1480), which has 24 sequence interruptions in the Gly-X-Y repeat up to 24 residues in length; and 3) the NC1 domain (residues 1481-1707), which is involved in the end-to-end assembly of collagen IV and is the most highly conserved domain of the protein. Alignment of the primary structure of the alpha 2(IV) chain with that of the alpha 1(IV) chain reported in the accompanying paper (Muthukumaran, G., Blumberg, B., and Kurkinen, M. (1989) J. Biol. Chem. 264, 6310-6317) suggests that a heterotrimeric collagen IV molecule contains 26 imperfections in the triple-helical domain. The proposed alignment is consistent with the physical data on the length and flexibility of collagen IV.
Esterases in Human Saliva (1975)

A sensitive method for quantitative determination of esterase activity has been applied to human saliva and used for substrate and inhibitor studies. By means of gel isoelectrofocusing the whole saliva esterases were divided into two main groups, each resolved into several bands. Comparison of isoelectrophoretic zymograms of whole, submandibular and parotid saliva indicates that one of the groups originates from the submandibular fluid. With the aid of gel filtration and ion-exchange chromatography the saliva esterases were partially separated and purified. The classification of the main saliva esterases as carboxylesterases (EC 3.1.1.1) is discussed in terms of their substrate and inhibitor properties.
A Dual-Microphone Speech Enhancement Algorithm Based on the Coherence Function (2011)

A novel dual-microphone speech enhancement technique is proposed in the present paper. The technique utilizes the coherence between the target and noise signals as a criterion for noise reduction and can be generally applied to arrays with closely-spaced microphones, where noise captured by the sensors is highly correlated. The proposed algorithm is simple to implement and requires no estimation of noise statistics. In addition, it offers the capability of coping with multiple interfering sources that might be located at different azimuths. The proposed algorithm was evaluated with normal hearing listeners using intelligibility listening tests and compared against a well-established beamforming algorithm. Results indicated large gains in speech intelligibility relative to the baseline (front microphone) algorithm in both single and multiple-noise source scenarios. The proposed algorithm was found to yield substantially higher intelligibility than that obtained by the beamforming algorithm, particularly when multiple noise sources or competing talker(s) were present. Objective quality evaluation of the proposed algorithm also indicated significant quality improvement over that obtained by the beamforming algorithm. The intelligibility and quality benefits observed with the proposed coherence-based algorithm make it a viable candidate for hearing aid and cochlear implant devices.
Synthesis and calcium channel modulating effects of modified Hantzsch nitrooxyalkyl 1,4‐dihydro‐2,6‐dimethyl‐3‐nitro‐4‐(pyridinyl or 2‐trifluoromethylphenyl)‐5‐pyridinecarboxylates (2000)

A group of racemic nitrooxyalkyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(pyridinyl or 2-trifluoromethylphenyl)-5-pyridinecarboxylates 8a–o were synthesized using modified Hantzsch reactions. In vitro calcium channel antagonist activities, determined using a guinea pig ileum longitudinal smooth muscle (GPILSM) assay, showed that compounds 8a–o exhibited weaker calcium antagonist activity (10–5 to 10–7 M range) than the reference drug nifedipine (IC50 = 1.43 × 10–8 M). Compounds 8 possessing a C-4 R1 = 2-pyridyl substituent were always more potent than the approximately equiactive analogs having an R1 = 3-pyridyl, 4-pyridyl or 2-CF3-C6H4-substituent, within each subgroup of nitrooxyalkyl compounds [R2 = – (CH2)nONO2 (n = 2, 3, 4) or –CH(CH2ONO2)2]. Although the length of the R2 = –(CH2)nONO2 substituent (n = 2–4) was not a determinant of smooth muscle calcium antagonist activity when the C-4 R1-substituent was 2-pyridyl, when R1 was a 3-pyridyl, 4-pyridyl, or 2-CF3-C6H4-substituent, the relative potency order with respect to the R2 = –(CH2)nONO2 substituent was n = 3 and 4 > n = 2. Replacement of the isopropyl substituent of the ester moiety of the calcium antagonist (±)-2-pyridyl 3a by a –(CH2)nONO2 (n = 2–4) moiety increased calcium antagonist activity on GPILSM by 8-fold. In contrast, replacement of the isopropyl substituent of the ester moiety of the calcium agonists (±)-3-pyridyl 3b, (±)-4-pyridyl 3c or the methyl substituent of the ester moiety of Bay K8644 by a R2 nitrooxyalkyl substituent resulted in abolition of their calcium agonist effects on GPILSM that is replaced by a smooth muscle calcium antagonist effect. These calcium antagonist data support the concept that incorporation of a nitrooxyalkyl ester substituent constitutes a valuable drug design strategy to enhance Hantzsch 1,4-dihydropyridine calcium antagonist and/or abolish calcium agonist effects on smooth muscle. Replacement of the isopropyl (8b–c), or the methyl (8d) group by a –CH2CH2ONO2 moiety resulted in retention of the cardiac positive inotropic effect where the relative potency order with respect to the C-4 substituent was 2-CF3-C6H6- (8d) > 3-pyridyl (8b) ≈ 4-pyridyl (8c). Model hybrid (calcium channel modulation, ·NO release) compounds, that exhibit dual cardioselective agonist / smooth muscle selective antagonist activities, represent a novel type of 1,4-dihydropyridine CC modulator that offers a potential approach to drug discovery targeted toward the treatment of congestive heart failure and for use as probes to study the structure–function relationship of calcium channels. Drug Dev. Res. 51:225–232, 2000. © 2001 Wiley-Liss, Inc.
A bleeding disorder due to deficiency of alpha 2-antiplasmin (1982)

Abstract A deficiency of alpha 2-antiplasmin has been identified in a female patient with severe and frequent bleeding episodes. Routine coagulation and platelet assays of the patient's plasma were within normal limits. However, abnormally rapid whole blood or dilute plasma clot lysis times and an abnormal FXIII test in which clots were lysed in the presence of urea or saline suggested an abnormal fibrinolytic system. Analysis of alpha 2-antiplasmin levels by radioimmunoassay revealed less than 1.0 microgram/ml alpha 2-antiplasmin. Functional assays indicated an alpha 2-antiplasmin level less than or equal to 10% of normal. Addition of purified alpha 2-antiplasmin to the patient's plasma restored its ability to inhibit plasmin in in vitro assays, and mixtures of patient plasma with normal plasma did not interfere with the antiplasmin activity of the normal plasma. Whereas normal platelets contain 68 ng alpha 2-antiplasmin/10(9) platelets, platelets from the patient contained 30% of the normal level of antigen. Analysis of alpha 2- antiplasmin functional and antigenic levels in the plasma of both parents and four siblings of the propositus provided evidence consistent with an autosomal mechanism of inheritance of alpha 2- antiplasmin deficiency. One sibling appeared to be homozygous and three siblings and the parents were heterozygous for the deficiency. Two heterozygotes had positive bleeding histories. The association of a bleeding disorder with a deficiency of alpha 2-antiplasmin emphasizes that lack of regulation of the fibrinolytic system can result in a hemostatic dysfunction.
Tunable resonant single-sideband electro-optical modulator (2009)

We demonstrate a broadly tunable and highly efficient resonant electro-optical modulator based on a whispering gallery mode resonator made with an electro optic crystal. This device is used to engineer a tunable opto-electronic oscillator.