gebhart/patrepeval huggingface dataset:
<i>Cis</i>-acting modifiers in the <i>ABCA4</i> locus contribute to the penetrance of the major disease-causing variant in Stargardt disease (2021)

Over 1200 variants in the ABCA4 gene cause a wide variety of retinal disease phenotypes, the best known of which is autosomal recessive Stargardt disease (STGD1). Disease-causing variation encompasses all mutation categories, from large copy number variants to very mild, hypomorphic missense variants. The most prevalent disease-causing ABCA4 variant, present in ~ 20% of cases of European descent, c.5882G > A p.(Gly1961Glu), has been a subject of controversy since its minor allele frequency (MAF) is as high as ~ 0.1 in certain populations, questioning its pathogenicity, especially in homozygous individuals. We sequenced the entire ~140Kb ABCA4 genomic locus in an extensive cohort of 644 bi-allelic, i.e. genetically confirmed, patients with ABCA4 disease and analyzed all variants in 140 compound heterozygous and 10 homozygous cases for the p.(Gly1961Glu) variant. A total of 23 patients in this cohort additionally harbored the deep intronic c.769-784C > T variant on the p.(Gly1961Glu) allele, which appears on a specific haplotype in ~ 15% of p.(Gly1961Glu) alleles. This haplotype was present in 5/7 of homozygous cases, where the p.(Gly1961Glu) was the only known pathogenic variant. Three cases had an exonic variant on the same allele with the p.(Gly1961Glu). Patients with the c.[769-784C > T;5882G > A] complex allele exhibit a more severe clinical phenotype, as seen in compound heterozygotes with some more frequent ABCA4 mutations, e.g. p.(Pro1380Leu). Our findings indicate that the c.769-784C > T variant is major cis-acting modifier of the p.(Gly1961Glu) allele. The absence of such additional allelic variation on most p.(Gly1961Glu) alleles largely explains the observed paucity of affected homozygotes in the population.
Mobile phone based acoustic localization for wireless sensor networks (2015)

In wireless sensor networks, localization techniques are required for finding physical location of the sensor nodes. Most of the existing 2D and 3D localization schemes are reference based. Finding physical locations of sensor nodes in an application field with only 2D or 3D physical topology map or logical topology map is arduous and tedious. This paper refers to mobile phone based acoustic localization technique for wireless sensor networks, which can be used along with physical topology map or logical topology map. In our proposed method, deployer searches the sensor node by using Doppler effect of acoustic wave, which is generated by his mobility. The proposed method helps in quick localizing of the sensor nodes without consuming much time and it has been implemented, tested by using mobile phone and IITH motes, the in-house developed sensor nodes.
Robust QAM classification against frequency offset (2010)

In this paper, the robust QAM classification method against phase offsets has been proposed. In the proposed method, the amplitude and the square cosine moments are used for the classification. The classification error probability has been examined for 16QAM and 64QAM. Simulation results have shown that the proposed method gives the superior classification performance to the amplitude moments method.
Glioblastoma Inhibition by Cell Surface Immunoglobulin Protein EWI-2, In Vitro and In Vivo (2009)

EWI-2, a cell surface IgSF protein, is highly expressed in normal human brain but is considerably diminished in glioblastoma tumors and cell lines. Moreover, loss of EWI-2 expression correlated with a shorter survival time in human glioma patients, suggesting that EWI-2 might be a natural inhibitor of glioblastoma. In support of this idea, EWI-2 expression significantly impaired both ectopic and orthotopic tumor growth in nude mice in vivo. In vitro assays provided clues regarding EWI-2 functions. Expression of EWI-2 in T98G and/or U87-MG malignant glioblastoma cell lines failed to alter two-dimensional cell proliferation but inhibited glioblastoma colony formation in soft agar and caused diminished cell motility and invasion. At the biochemical level, EWI-2 markedly affects the organization of four molecules (tetraspanin proteins CD9 and CD81 and matrix metalloproteinases MMP-2 and MT1-MMP), which play key roles in the biology of astrocytes and gliomas. EWI-2 causes CD9 and CD81 to become more associated with each other, whereas CD81 and other tetraspanins become less associated with MMP-2 and MT1-MMP. We propose that EWI-2 inhibition of glioblastoma growth in vivo is at least partly explained by the capability of EWI-2 to inhibit growth and/or invasion in vitro. Underlying these functional effects, EWI-2 causes a substantial molecular reorganization of multiple molecules (CD81, CD9, MMP-2, and MT1-MMP) known to affect proliferation and/or invasion of astrocytes and/or glioblastomas.
Cervical Spine Hyperextension and Altered Posturo-Respiratory Coupling in Patients With Obstructive Sleep Apnea Syndrome (2020)

Obstructive sleep apnea syndrome (OSAS) is associated with postural dysfunction characterized by abnormal spinal curvature and disturbance of balance and walking, whose pathophysiology is poorly understood. We hypothesized that it may be the result of a pathological interaction between postural and ventilatory functions. Twelve patients with OSAS (4 women, age 53 years [51-63] (median [quartiles]), apnea hypopnea index 31/h [24-41]) were compared with 12 healthy matched controls. Low dose biplanar X-rays (EOS® system) were acquired and personalized three-dimensional models of the spine and pelvis were reconstructed. We also estimated posturo-respiratory coupling by measurement of respiratory emergence, obtaining synchronized center of pressure data from a stabilometric platform and ventilation data recorded by an optico-electronic system of movement analysis. Compared with controls, OSAS patients, had cervical hyperextension with anterior projection of the head (angle OD-C7 12° [8; 14] vs. 5° [4; 8]; <i>p</i> = 0.002), and thoracic hyperkyphosis (angle T1-T12 65° [51; 71] vs. 49° [42; 59]; <i>p</i> = 0.039). Along the mediolateral axis: (1) center of pressure displacement was greater in OSAS patients, whose balance was poorer (19.2 mm [14.2; 31.5] vs. 8.5 [1.4; 17.8]; <i>p</i> = 0.008); (2) respiratory emergence was greater in OSAS patients, who showed increased postural disturbance of respiratory origin (19.2% [9.9; 24.0] vs. 8.1% [6.4; 10.4]; <i>p</i> = 0.028). These results are evidence for the centrally-mediated and primarily respiratory origin of the postural dysfunction in OSAS. It is characterized by an hyperextension of the cervical spine with a compensatory hyperkyphosis, and an alteration in posturo-respiratory coupling, apparently secondary to upper airway instability.
Data Supplement from Intraperitoneal Oxidative Stress in Rabbits with Papillomavirus-Associated Head and Neck Cancer Induces Tumoricidal Immune Response That Is Adoptively Transferable (2023)

&lt;p&gt;Supplementary Table 2B. Complete RT2 Profiler PCR Array 2. Overview of all genes analyzed by the RT2 Profiler PCR Array (SABiosciences, PANZ-052ZA). Fold changes of mRNA expression level measured in remitting VX2 tumors in the cause of the O3/O2-PP therapy (Regression, n=6) were calculated in reference to mRNA level measured in growing VX2 tumors of sham treated animals (Progression, n=6). Regulation of mRNA level is marked by â†‘ (up) or â†“ (down). Statistic differences were calculated by the paired t-test and marked as: *p&lt;0.05; **p&lt;0.01; ***p&lt;0.001; n.s. not significant.&lt;/p&gt;
The cognitive flexibility scale: Three validity studies (1998)

The complexities of everyday life reinforce the need to be cognitively flexible. Cognitive flexibility refers to a person's awareness of communication alternatives, willingness to adapt to the situation, and self‐efficacy in being flexible. Three studies were conducted to establish further the validity of the Cognitive Flexibility Scale (Martin & Rubin, 1995). In Study One, cognitive flexibility was positively related to two other identified constructs of communication competence, assertiveness and responsiveness. In Study Two, respondents’ assessments of their own cognitive flexibility were positively related to ratings from their friends. In Study Three, a positive relationship was found between being cognitively flexible and confidence in performing communication behaviors.
A switching control scheme for constrained robot tasks (2002)

The paper presents the design and real-time control implementation issues of a switching control scheme for a robot interacting with a constraint surface. One key aspect investigated is the effect of uncertainty in the location of the constraint surface. A switching controller that is robust to uncertainty in the location of the constraint surface is given for a typical constrained robot task. Further, a strategy for real-time trajectory modification, which is required to compensate for the discrepancy in the a-priori known location and the actual location of the constraint, is given. Details of the experimental platform and typical experimental results are given. This research can find applications in robotic surface finishing operations such as polishing, chamfering and deburring, etc.
Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels (2019)

Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.
The Clinical Pharmacology and Use of Paroxetine, a New Selective Serotonin Reuptake Inhibitor (1994)

Major depression afflicts a significant percentage of the population, and optimum therapy is often limited by the poor tolerability and lethality in overdose of the tricyclic antidepressants. The selective serotonin reuptake inhibitors (SSRIs) fluoxetine, sertraline, and, more recently, paroxetine are viewed as welcome additions to existing therapy. The SSRIs are as effective as the tricyclic antidepressants, but are not associated with their adverse effect profile. Paroxetine in dosages of 20-50 mg/day is as effective as the older classic antidepressants, including amitriptyline, imipramine, and doxepin. It is effective in the elderly and in patients with recurrent, resistant, or severe depression.
Comparative Evaluation of ARCP and Three-Level TCM Soft-Switching Bridge-Legs for High-Frequency SiC Converter Systems (2022)

Soft-switching bridge-legs facilitate high-efficiency three-phase PV inverters or PFC rectifiers. By extending a half-bridge with a resonant auxiliary circuit, including two additional transistors, zero-voltage switching (ZVS) of the main transistors can be realized (Active Resonant Commutated Pole, ARCP). Alternatively, a similar T-type bridge-leg structure achieves ZVS by operating the output filter inductor with a sufficiently high current ripple (with 3-level Triangular Current Modulation, 3L-TCM). We provide a comparative evaluation of these two concepts for the realization of 2.2 kW (per phase), 800 V DC bridge-legs with latest-generation 1200 V and 650 V SiC MOSFETs, discussing chip-area optimization, filter design for compliance with current and future EMI limits, and qualitative limits and design criteria. The calculated loss-vs.-volume Pareto fronts indicate advantages for the 3L-TCM approach, with peak switching frequencies of 72 kHz or 144 kHz and an efficiency (semiconductors and EMI filter) of about 99.6 %. The ARCP concept seems more suitable for applications that do not necessarily require EMI filters but benefit from limited switch-node <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$dv/dt$</tex> (in the order of 1.5 V/ns) such as variable-speed drives.
Effects of External Pressure on the Performance of Lithium Anode Cells (2018)

Rechargeable lithium metal anode batteries (RLB) have the potential to meet the Department of Energy’s 500 Wh/kg goal [1]. However, higher cycling efficiency and safety of these cells is challenged by the dendritic Li plating morphology. Li surface protective coating or electrolyte that can promote growth of stable solid electrolyte interphase from the reduction products can prevent dendritic growth of Li during plating. Another way to suppress the dendritic growth and facilitate more uniform Li surface morphologies is by applying the external pressure to the cell [2]. The external cell pressure can influence the Li plating conditions and modify Li surface. The growth of Li dendrites can be suppressed due to the Li surface strain field under external cell pressure. Also the loss due to dead lithium can be minimized by maintaining a good electrochemical contact between Li deposits. A dendrite-free uniform mossy Li surface with good electrochemical contact will improve the cycling efficiency and safety of the cells. The effect of external cell pressure was studied in cells with nickel rich LiNi 0.6 Mn 0.2 Co 0.2 O 2 cathode and Li metal anode. The cycling performance was analyzed with electrochemical diagnostics tools. The Li surface morphology was characterized with scanning electron microscopy. The effects of various external pressure on cycling efficiency and the Li surface morphology will be illustrated and discussed. References: [1] Battery500 Consortium to Spark EV Innovations: Pacific Northwest National Laboratory-led, 5-year $50M effort seeks to almost triple energy stored in electric car batteries, in Office of Technology Transitions Energy.gov (2016). [2] Gireaud, L., Grugeon, S., Laruelle, S., Yrieix, and B., Tarascon, J. –M., Electrochem. Comm. 8, 1639–1649 (2006)
Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content  (2003)

Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.
Non-ionic photoacid generators for chemically amplified resists: evaluation results on the application-relevant properties (2007)

Recently we have developed and reported some novel non-ionic photoacid generators (PAGs) which generate a strong acid (perfluorobutanesulfonic acid) by light irradiation and is applicable to chemically amplified ArF photoresist, such as 2-[2,2,3,3,4,4,5,5-octafluoro-1-(nonafluorobutylsulfonyloxyimino)-pentyl]-fluorene (ONPF), 2- [2,2,3,3,4,4,4-heptafluoro-1-(nonafluorobutylsulfonyloxyimino)-butyl]-fluorene (HNBF) and so on. Here the lithographic property of ONPF in some ArF model formulations was evaluated under 193 nm dry and immersion exposure comparing one of the most typical ionic PAGs, triphenylsulfonium perfluorobutanesulfonate (TPSPB), on lithographic application-relevant properties, e.g. exposure latitude, line edge roughness (LER) and so on, by top-down view SEM observation. 80 nm line and space (L/S) patterning was successfully conducted. Additionally we investigated the striation issue with ONPF when the matrix polymer of resist was changed. It was revealed that ONPF showed better coating property in a copolymer of &ggr;-butyrolactone methacrylate, 2-ethyladamantyl methacrylate and hydroxyladamantyl methacrylate than in a copolymer of &dgr;-methacryloyloxynorbornane butyrolactone in lactone unit.
Expanding the Morphological and Molecular Genetic Phenotype of Kidney Cancer (2006)

No AccessJournal of UrologyEditorial1 Jan 2007Expanding the Morphological and Molecular Genetic Phenotype of Kidney Canceris companion ofImpact of Tumor Size on the Predictive Ability of the pT3a Primary Tumor Classification for Renal Cell Carcinomap21 is a Prognostic Marker for Renal Cell Carcinoma: Implications for Novel Therapeutic Approaches Manish Vira and W. Marston Linehan Manish ViraManish Vira More articles by this author and W. Marston LinehanW. Marston Linehan More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2006.10.011AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Expanding the Morphological and Molecular Genetic Phenotype of Kidney Cancer." The Journal of Urology, 177(1), pp. 10–11 References 1 : Cancer statistics, 2006. CA Cancer J Clin2006; 56: 106. Google Scholar 2 : Comprehensive Textbook of Genitourinary Oncology. Philadelphia: Lippincott Williams & Wilkins2006. Google Scholar 3 : Current TNM classification of renal cell carcinoma evaluated: revising stage T3a. J Urol2005; 173: 33. Link, Google Scholar 4 : Reevaluation of TNM staging of renal cortical tumors: recurrence and survival for T1N0M0 and T3aN0M0 tumors are equivalent. Urology2006; 68: 287. Google Scholar 5 : Kidney cancer: identification of novel targets for therapy. Kidney Int2006; 69: 224. Google Scholar 6 : The genetic basis of cancer of the kidney. J Urol2003; 170: 2163. Link, Google Scholar 7 : Genetic basis of cancer of the kidney: disease-specific approaches to therapy. Clin Cancer Res2004; 10: 6282S. Google Scholar 8 : Focus on kidney cancer. Cancer Cell2004; 6: 223. Google Scholar National Cancer Institute, Bethesda, Maryland© 2007 by American Urological AssociationFiguresReferencesRelatedDetailsRelated articlesJournal of Urology9 Nov 2018Impact of Tumor Size on the Predictive Ability of the pT3a Primary Tumor Classification for Renal Cell CarcinomaJournal of Urology9 Nov 2018p21 is a Prognostic Marker for Renal Cell Carcinoma: Implications for Novel Therapeutic Approaches Volume 177Issue 1January 2007Page: 10-11 Advertisement Copyright & Permissions© 2007 by American Urological AssociationMetrics Author Information Manish Vira More articles by this author W. Marston Linehan More articles by this author Expand All Advertisement PDF downloadLoading ...
Management of a Pregnant Patient with an Open Abdomen (2005)

Aboutanos, Sharline Z. MD; Aboutanos, Michel B. MD, MPH; Malhotra, Ajai K. MD; Duane, Therese M. MD; Ivatury, Rao R. MD Author Information
Determinants of Human Papillomavirus Infection Among Inuit Women of Northern Quebec, Canada (2010)

We investigated risk factors for prevalent high-risk human papillomavirus (HR-HPV) in Inuit women from Quebec. Younger age and having 10 or more lifetime sexual partners were associated with HR-HPV. Findings suggest that for older women, markers of recent sexual activity are more predictive of HR-HPV status than markers of lifetime sexual history.
ChemInform Abstract: Mild and Efficient Tetrahydropyranylation of Alcohols — Catalysis by Lithium Perchlorate in Diethyl Ether. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Evaluation of the diagnostic potential of<i>ex vivo</i>Raman spectroscopy in gastric cancers: fingerprint versus high wavenumber (2016)

The aim of this study was to apply Raman spectroscopy in the high wavenumber (HW) region (2800 to 3000??cm?1) for ex vivo detection of gastric cancer and compare its diagnostic potential with that of the fingerprint (FP) region (800 to 1800??cm?1). Raman spectra were collected in the FP and HW regions to differentiate between normal mucosa (n=38) and gastric cancer (n=37). The distinctive Raman spectral differences between normal and cancer tissues are observed at 853, 879, 1157, 1319, 1338, 1448, and 2932??cm?1 and are primarily related to proteins, lipids, nucleic acids, collagen, and carotenoids in the tissue. In FP and HW Raman spectroscopy for diagnosis of gastric cancer, multivariate diagnostic algorithms based on partial-least-squares discriminant analysis, together with leave-one-sample-out cross validation, yielded diagnostic sensitivities of 94.59% and 81.08%, and specificities of 86.84% and 71.05%, respectively. Receiver operating characteristic analysis further confirmed that the FP region model performance is superior to that of the HW region model. Better differentiation between normal and gastric cancer tissues can be achieved using FP Raman spectroscopy and PLS-DA techniques, but the complementary natures of the FP and HW regions make both of them useful in diagnosis of gastric cancer.