gebhart/patrepeval huggingface dataset:
Comparative performance of static-mode ferrous MEMS gradiometers fabricated by a three-step DRIE process (2010)

Two MEMS structures—a cantilever beam and a quad-beam—have been designed and fabricated through a three-step deep reactive ion etching (DRIE) process. Devices feature target patterns to align with an external optical detection system and a micromachined cavity to embed an NdFeB hard mini-magnet, thus releasing the stress of structures. Structures are intended for magnetostatic gradient measurements. Induced magnetic fields generate an attracting force on the magnet that deflects the sensor. Deflection is optically detected through nanometer-resolution confocal microscopy. The static-mode sensitivity of up to 1.86 × 10−4 T m−1 demonstrates that MEMS gradiometers are able to perform in situ gradiometry with a single sensor and miniaturized size. Suitable techniques for integrated detection are discussed.
Clinical presentation and treatment of bladder pain syndrome/interstitial cystitis (BPS/IC) in India. (2015)

Bladder pain syndrome/interstitial cystitis (BPS/IC) is a chronic disease characterized by pelvic pain urgency and frequency. Patients with severe symptoms lead a very miserable life. North American, European and Asian guidelines have been recently promulgated but they differ on many important issues. There is no consensus on its name, definition, investigations and management. Indian guidelines have also been developed and they give more importance to the symptoms in relation to micturition. Though initially believed to be rare or non-existent in India the situation has changed. In Indian patients the presentation is more or less same as the rest of the world but a large percentage have obstructive symptoms and unusual urinary symptoms. Anal discomfort is also common. In India the commonest investigation in all cases of lower urinary tract (LUT) dysfunction is ultrasonography of kidney ureter and bladder with measurement of the post void residual urine volume. Cystoscopy is also done in all the cases to rule out presence of tuberculosis or carcinoma in situ. Bladder pain syndrome/interstitial cystitis (BPS/IC) is not considered to be a clinical disease as it is difficult to rule out all differential diagnosis only from history. Hunner's lesion is very rare. Cystoscopy with hydro distension, oral therapy, intravesical therapy and surgical therapy form the back bone of management. It is difficult to know which treatment is best for a given patient. A staged protocol is followed and all the treatment modalities are applied to the patients in a sequential fashion-starting from the non-invasive to more invasive. Intravesical botox has not been found to be effective and there is no experience with interstim neuromodulation.
Site-directed mutagenesis of the alpha-toxin gene of Staphylococcus aureus: role of histidines in toxin activity in vitro and in a murine model (1994)

Staphylococcus aureus alpha-toxin is a membrane-damaging exoprotein that oligomerizes to form transmembrane pores. Chemical modification of histidines with diethylpyrocarbonate has been shown to reduce the hemolytic activity of alpha-toxin, suggesting that one or more of the histidine residues is important for toxin function. To individually assess the functional importance of each of the four histidine residues (residues 35, 48, 144, and 259), we used oligonucleotide-directed mutagenesis of the cloned alpha-toxin gene to replace each histidine with leucine. The mutant toxins were expressed in S. aureus and evaluated for hemolytic activity in vitro and for lethality in an intraperitoneal murine model. Substitution of histidine 35 with leucine produced a mutant toxin (H35L) without hemolytic or lethal activity. Mutant toxins H48L, H144L, and H259L exhibited 7, 16, and 46%, respectively, of the hemolytic activity of wild-type toxin. Immunoblotting of purified H35L toxin incubated with liposomal membranes demonstrated intact membrane binding and hexamer formation that was clearly detectable but reduced compared with that of the wild-type toxin. This suggests that hexamer formation alone is not sufficient for the expression of alpha-toxin activity. The nature of the defect underlying the lack of activity of the H35L mutant toxin remains to be elucidated but may involve failure of the hexamer to span the lipid bilayer to form a transmembrane pore or a change in the internal surface and permeability characteristics of the pore.
Real-time dynamic focusing through tissue inhomogeneities during hyperthermia treatments with phased arrays (1994)

A needle probe hydrophone array made of discrete PVDF elements has been designed and fabricated at our laboratory. Such a probe can obtain complex acoustic pressure measurements at or near the tumor site. To extend the region over which these measurements may be used to focus a phased array, a real-time measurement system is needed, along with a method of extrapolating the data to points other than those measured by the probe. We describe such a real-time dynamic focusing algorithm that uses measurements from the full-set of hydrophone array elements in estimating the bearing and range of the elements of the transmitting array. In this way, a measurement of the radius of curvature of the wave front due to an array element is made along the span of the array, which extends the region of reliable refocusing. An outline of the steps of the refocusing algorithm along with simulation and experimental results are given. Finally, we describe the architecture of a real-time system for refocusing currently being designed for this purpose
Synthesis of oligonucleotides via monomers with unprotected bases (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of oligonucleotides via monomers with unprotected basesSergei M. Gryaznov and Robert L. LetsingerCite this: J. Am. Chem. Soc. 1991, 113, 15, 5876–5877Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/ja00015a059https://doi.org/10.1021/ja00015a059research-articleACS PublicationsRequest reuse permissionsArticle Views523Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Characterization of an anti-Trop-2-SN-38 antibody-drug conjugate (IMMU-132) with potent activity against solid cancers. (2014)

3107 Background: IMMU-132 is an antibody-drug conjugate (ADC) made from a humanized anti-Trop-2 mAb (hRS7) coupled through a linker to SN-38, the active metabolite of CPT-11. Trop-2 is found in a wide range of tumor, including gastric, pancreatic, triple-negative breast (TNBC), colonic, prostate, and lung. Current Phase I/II clinical trials confirm the anticancer activity of IMMU-132 in cancers expressing Trop-2. The current studies further characterize IMMU-132 in terms of conjugation, mechanism of action (MoA), and efficacy. Methods: SN-38 conjugation to hRS7 was analyzed by HIC, LC-MS, and HPLC. MoA was assessed by comparisons in binding, ADCC, and pro-apoptotic signaling pathways. Efficacy studies were performed in mice bearing human tumor xenografts. Results: IMMU-132 has a drug to antibody ratio of 7.6, <1% aggregation, and no loss in binding to cells or to a Trop-2 chip (cells: KD = 0.63 ± 0.26 nM v 0.54 ± 0.17 nM; BIACore: 0.26 ± 0.14 v 0.51 ± 0.04 nM, IMMU-132 and hRS7, respectively). Linkage chemistry should preserve the active lactone ring form; initial in vivo data suggest that conjugated SN-38 may not be glucuronidated until released. IMMU-132 retains binding to the neonatal receptor, but lost 65% of ADCC activity. Free SN-38 and IMMU-132 mediated the same signaling pathways in cells, with p21WAF1/Cip1 up-regulation, cleavage of caspase 3 and 9, and poly-ADP-ribose polymerase cleavage. IMMU-132 treatment of gastric cancer xenografts (17.5 mg/kg; 2xwk x 4wks) result in significant anti-tumor effects compared to non-specific control ADC (P<0.0001). In tumors not typically treated with irinotecan as a single agent (pancreatic and TNBC), IMMU-132 provided significant tumor growth inhibition. Mice with a TNBC xenograft treated with 12.5 mg/kg IMMU-132 (q4dx4) resulted in 7/8 mice alive at study conclusion (day 105) v only 1/9 in saline-control group (P=0.001). Tumor regressions occur in mice bearing aggressive pancreatic tumor xenografts (untreated median survival = 11 d) when clinically relevant doses of IMMU-132 is given (HED=8 mg/kg; P=0.0003). Conclusions: Conjugation of SN-38 to hRS7 results in a potent ADC that retains characteristics of both the antibody and the drug.
Breast Cancer Molecular Signatures as Determined by SAGE: Correlation with Lymph Node Status (2007)

Global gene expression measured by DNA microarray platforms have been extensively used to classify breast carcinomas correlating with clinical characteristics, including outcome. We generated a breast cancer Serial Analysis of Gene Expression (SAGE) high-resolution database of approximately 2.7 million tags to perform unsupervised statistical analyses to obtain the molecular classification of breast-invasive ductal carcinomas in correlation with clinicopathologic features. Unsupervised statistical analysis by means of a random forest approach identified two main clusters of breast carcinomas, which differed in their lymph node status (P=0.01); this suggested that lymph node status leads to globally distinct expression profiles. A total of 245 (55 up-modulated and 190 down-modulated) transcripts were differentially expressed between lymph node (+) and lymph node (-) primary breast tumors (fold change, >or=2; P<0.05). Various lymph node (+) up-modulated transcripts were validated in independent sets of human breast tumors by means of real-time reverse transcription-PCR (RT-PCR). We validated significant overexpression of transcripts for HOXC10 (P=0.001), TPD52L1 (P=0.007), ZFP36L1 (P=0.011), PLINP1 (P=0.013), DCTN3 (P=0.025), DEK (P=0.031), and CSNK1D (P=0.04) in lymph node (+) breast carcinomas. Moreover, the DCTN3 (P=0.022) and RHBDD2 (P=0.002) transcripts were confirmed to be overexpressed in tumors that recurred within 6 years of follow-up by real-time RT-PCR. In addition, meta-analysis was used to compare SAGE data associated with lymph node (+) status with publicly available breast cancer DNA microarray data sets. We have generated evidence indicating that the pattern of gene expression in primary breast cancers at the time of surgical removal could discriminate those tumors with lymph node metastatic involvement using SAGE to identify specific transcripts that behave as predictors of recurrence as well.
污染河流 用于现场评价和修复的地貌学-地化学方法 (2007)

河流污染是一个受全球关注的普遍问题。某些受污染河段可以覆盖河道河床和相邻河谷平原的几十公里，其修复正日益受到重视。河流修复后的评估结果表明：亟待将对河流流域地貌和地面过程的了解整合到现场特征描述、评价和修复策略中。
15 RNA Editing: New Uses for Old Players in the RNA World (1993)

The sequence of a cellular RNA cannot always be inferred from the gene that encodes it. Subsequent to transcription, certain RNAs are edited. RNA editing can involve the insertion or deletion of nucleotides, as well as the modification of encoded nucleotides. RNA editing is required in certain mRNAs to create initiation and termination codons, as well as to eliminate internal frameshifts and change the identity of internal amino acids. Recently, RNA editing has also been observed in certain tRNAs and rRNAs; here the edited residues appear to be necessary to maintain the three-dimensional structure that is crucial to the function of these RNAs. At present, RNA editing has only been observed in eukaryotes, but in this kingdom it is widespread and found in mitochondrion-encoded RNAs of kinetoplastids, slime molds, and plants; chloroplast-encoded RNAs of plants; and nucleus-encoded RNAs of mammals (Table 1). Although once thought to be limited to the insertion and deletion of uridine residues, editing reactions that produce non-encoded adenosines, guanosines, cytidines, and possibly inosines, have now been described. The discovery of each new example of editing begins with the observation that a genomic sequence does not correlate with the corresponding cDNA sequence. The discovery of so many examples of RNA editing in recent years is the result of technological advances in sequencing and the polymerase chain reaction (PCR). This review does not focus on the methodology behind the identification of edited transcripts, but rather on the subsequent studies performed to elucidate the mechanisms involved in the editing...
Microseismic Monitoring: Inside and Out (2009)

Distinguished Author Series articles are general, descriptive representations that summarize the state of the art in an area of technology by describing recent developments for readers who are not specialists in the topics discussed. Written by individuals recognized as experts in the area, these articles provide key references to more definitive work and present specific details only to illustrate the technology. Purpose: to inform the general readership of recent advances in various areas of petroleum engineering. Abstract Since its inception in the 1970s and its commercialization circa 2000, microseismic monitoring has proved to be an invaluable tool for understanding underground processes. While its most common and notable use has been hydraulic-fracture mapping, it also is used for reservoir monitoring of thermal processes, drill-cuttings injection, geothermal hot-dry- rock stimulations, reservoir surveillance, and many other processes in oil and gas and mining. Fig. 1 shows a typical layout for a monitoring test, with the offset monitoring well at some reasonable distance from the fracture (inset) and a receiver array somewhere near the depth of the fracture treatment. Because the amplitude of the microseism decays with distance, there is a maximum monitoring distance that can be used in any test with respect to both horizontal and vertical positioning. Designed correctly, this type of monitoring can provide information on fracture height, length, azimuth, asymmetry, dip, and complexity, which can be used to optimize the fracture design and field development. To most outsiders, the entire process of microseismic monitoring appears to be something of an art, and the "what," "why," and "how" details are not very clear even though there have probably been more than 6,000 fracture treatments monitored since 2000, in rocks ranging from tight sandstones and gas shales to carbonates and even volcanic, and at depths ranging from several hundred feet to more than 13,000 ft. The purpose of this article is to lay out a basic framework for planning, executing, analyzing, and interpreting a microseismic mapping project and, hopefully, add some rigor to the process that can be used for guidelines or standards. Overview Basically, microseismic monitoring is the placement of receiver systems in advantageous positions from which small earthquakes (microseisms) induced by some downhole process can be detected and located to provide geometric and behavioral information about the process. In the case of hydraulic fracturing—the process of primary concern here— a sensitive-receiver array having numerous levels typically is placed in an offset well at a depth relatively close to the process. This array detects the seismic energy generated by the microseism by use of three-component geophones or accelerometers, and then algorithms are processed to locate the "event" using an assortment of information obtained from compressional (P-wave) and shear (S-wave) arrivals detected by the array.
A distributed launch and recovery system for an AUV and a manned submersible (2003)

The launch and recovery (L&R) of an autonomous underwater vehicle (AUV) by a manned submersible (MS) is required for joint AUV/MS missions. The authors consider L&R as a distributed artificial intelligence (DAI) task. The approach has been taken to provide assistance in definition of subtasks, allocation of task responsibility, and specification of required data acquisition, processing, and communication. An architecture for the task requires special-purpose communications and multi-agent planning. The authors define the problem, the agents. the goals and constraints, review DAI, and discuss some real-world experiences. Three candidate DAI architectures are examined, and a hybrid, consisting of elements of all three, is suggested for further investigation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solvent Replacement for Green Processing (1998)

Julie Sherman, Bain Chin, Paul D. T. Huibers, Ricard Garcia-Valls, T. Alan Hatton, Solvent Replacement for Green Processing, Environmental Health Perspectives, Vol. 106, Supplement 1 (Feb., 1998), pp. 253-271
ASIC implementation of the Lyon cochlea model (1992)

The design and development of an application-specific integrated circuit (ASIC) to implement the filtering and AGC sections of a new digital approximation to the Lyon/Mead analog cochlea model (1988, 1989) are described. The ASIC uses a fully synchronous bit-serial design methodology originally developed for MOS technologies by Denyer and Renshaw (1985) and adaptive subsequently for use with low cost standard cell design tools by Summerfield and Jabri (1989). The resulting device is an example of a new class of signal processing ASIC, referred to as an application-specific signal processor (ASSP). As well as presenting details of the filter and AGC structure of the new cochlea model, the paper describes the bit-serial design methodology used to implement the algorithm in real-time and in low cost ASIC form. The approach is a generic one and can be applied to a wide range of speech signal processing functions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
TNF-α antagonists: monoclonal antibodies, soluble receptors, thalidomide and other novel approaches (1997)

Tumour necrosis factor-alpha (TNF-alpha) is a pleiotropic molecule produced in response to a variety of stimuli during normal host defence. At low levels, TNF-alpha confers protection against infectious agents, tumours and tissue damage, and plays a role in the development of humoral immunity. However, overproduction of TNF-alpha has been implicated in the pathogenesis of a wide variety of conditions, including autoimmunity, malignancy, inflammatory and immunopathological diseases. Furthermore, TNF-alpha is a key regulator of other pro-inflammatory cytokines; infiltrating mononuclear cells that produce excessive amounts of TNF-alpha at sites of inflammation are, therefore, primary targets for therapeutic intervention. Traditional anti-inflammatory drugs, such as cyclosporin, have widespread immunosuppressive effects and are now being replaced by more specific anti-TNF-alpha compounds. In this report, work presented at the recent Cambridge Symposia meeting on TNF-alpha antagonists in Santa Fe, New Mexico, will be highlighted and discussed.
<title>Capture-time indexing paradigm, authoring tool, and browsing environment for digital broadcast video</title> (1995)

Historically, Multimedia Video-on-Demand (VOD) systems have considered stream indexing as an authoring activity, decomposing monolithic streams containing no explicit indexing information. This paper suggests a scheme for 'up-front,' capture-time indexing of digital video streams, whereby the indexing information logically becomes part of the stream. This approach takes advantage of the sequential, temporal nature of capture and the knowledge of the stream recorder to empower further manipulation and playout of the stream. We explore the impact of capture-time indices, and implement a sample format in a Segment Definition File (SDF). The Video Broadcast Authoring Tool (VBAT) is the focus of our paper. Taking a video stream and an SDF as input, VBAT provides a means for authors to create, delete, modify and annotate segments of that stream. VBAT also integrates existing technology such as World-Wide Web's HTTP links and the Motion Picture Parser application. Creation of various-format stills for browsing is supported. VBAT provides for post-processing of the SDF to various playout environments; we implement and describe a postprocessor for World-Wide Web browsing and playout. Finally, we discuss VBAT's position in an integrated digital video broadcast environment and areas of future work.
Molecular docking and 3D-QSAR studies on inhibitors of DNA damage signaling enzyme human PARP-1 (2012)

Poly (ADP-ribose) polymerase-1 (PARP-1) operates in a DNA damage signaling network. Molecular docking and three dimensional-quantitative structure activity relationship (3D-QSAR) studies were performed on human PARP-1 inhibitors. Docked conformation obtained for each molecule was used as such for 3D-QSAR analysis. Molecules were divided into a training set and a test set randomly in four different ways, partial least square analysis was performed to obtain QSAR models using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Derived models showed good statistical reliability that is evident from their r², q²(loo) and r²(pred) values. To obtain a consensus for predictive ability from all the models, average regression coefficient r²(avg) was calculated. CoMFA and CoMSIA models showed a value of 0.930 and 0.936, respectively. Information obtained from the best 3D-QSAR model was applied for optimization of lead molecule and design of novel potential inhibitors.
Orchiectomy for suspected microscopic tumor in patients with anti-Ma2-associated encephalitis (2006)

In young men with Ma2-encephalitis, 1) the disorder should be attributed to a germ-cell neoplasm of the testis unless another Ma2-expressing tumor is found, 2) negative tumor markers, ultrasound, body CT, or PET do not exclude an intratubular germ-cell neoplasm of the testis, and 3) if no tumor is found, the presence of the five indicated criteria should prompt consideration of orchiectomy.
5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis. (1993)

The structure of the non-self-complementary DNA heptamer d(CGACGAC) at low pH has been determined by the quantitative NMR refinement procedure designated SPEDREF (SPEctral-Driven REFinement). Acid-base titration of the molecule indicated a prominent n = 2 pKa near 6.8. In the pH range up to 6.0, the heptamer forms a remarkably stable double helix, which was conclusively shown to be an unusual homobase-paired parallel-stranded double helix (termed II-DNA). In this II-DNA helix, the 5'-CGA trinucleotide is the structural motif that accounts for the stability, with the C+-C hemiprotonated base pair (in which C+ is N3-protonated cytosine) providing for the alignment site and the unusual interstrand G-A base stack in the GpA step furnishing the additional stabilizing forces. The exchangeable proton data from two-dimensional nuclear Overhauser effect spectroscopy are in total agreement with the refined structure. We conclude that the 5'-CGA or other related sequences (e.g., 5'-CCGA) are powerful motifs in promoting the II-DNA or II-RNA conformations that may play certain biological functions.