gebhart/patrepeval huggingface dataset:
Retinitis pigmentosa prior to familial ALS caused by a homozygous cilia and flagella-associated protein 410 mutation (2019)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by the loss of both upper and lower motor neurons. Approximately 10% of patients with ALS have a family history of the disease, and 22 genes have already been reported to be implicated in ALS.1 In previous reports, some of the genes implicated in ALS were associated with visual dysfunctions; however, no cases have yet reported patients presenting clinically both ALS and ocular abnormalities.1 

Recently, a large case-controlled genome-wide association study (GWAS) of ALS revealed cilia and flagella-associated protein 410 ( CFAP410 ), previously called as C21orf2 .2 CFAP410 is causative for axial spondylometaphyseal dysplasia (SMDAX), which presents with retinitis pigmentosa (RP), and retinal dystrophy (RD) with or without macular staphyloma.3 However, no hereditary ALS cases have yet reported CFAP410 variants.

In this letter, we provide the first description of siblings with RP and ALS with the causative CFAP410 mutation. They showed RP until their fourth decade and muscle weakness of the extremities started more than 10 years after the diagnosis of RP.

The pedigree chart of the affected family is presented in figure 1A. Their parents (I-1 and I-2) were consanguineous and neurologically healthy.



Figure 1 
(A) Pedigree chart of the affected family. Shaded boxes represent affected members. Symbols having diagonal lines represent deceased individuals. Unaffected family members exhibited no abnormalities during their medical examinations. (B) Sanger sequencing revealed that the patients had exon 4 of a CFAP410 homozygous variant (c.319T>C, p.Y107H) and that the non-affected sibling had a heterozygous variant of CFAP410 . (C) Heterozygous CFAP410 variants of amyotrophic lateral sclerosis (ALS) (black) were previously detected except for exon 2. On the other hand, causative …
Zips (2013)

We propose a streaming algorithm, based on the minimal description length (MDL) principle, for extracting non-redundant sequential patterns. For static databases, the MDL-based approach that selects patterns based on their capacity to compress data rather than their frequency, was shown to be remarkably effective for extracting meaningful patterns and solving the redundancy issue in frequent itemset and sequence mining. The existing MDL-based algorithms, however, either start from a seed set of frequent patterns, or require multiple passes through the data. As such, the existing approaches scale poorly and are unsuitable for large datasets. Therefore, our main contribution is the proposal of a new, streaming algorithm, called Zips, that does not require a seed set of patterns and requires only one scan over the data. For Zips, we extended the Lempel-Ziv (LZ) compression algorithm in three ways: first, whereas LZ assigns codes uniformly as it builds up its dictionary while scanning the input, Zips assigns codewords according to the usage of the dictionary words; more heaviliy used words get shorter code-lengths. Secondly, Zips exploits also non-consecutive occurences of dictionary words for compression. And, third, the well-known space-saving algorithm is used to evict unpromising words from the dictionary. Experiments on one synthetic and two real-world large-scale datasets show that our approach extracts meaningful compressing patterns with similar quality to the state-of-the-art multi-pass algorithms proposed for static databases of sequences. Moreover, our approach scales linearly with the size of data streams while all the existing algorithms do not.
Polygon Shape Formation for Multi-Mobile Robots in a Global Knowledge Environment (2019)

In coordination of a group of mobile robots in a real environment, the formation is an important task. Multimobile robot formations in global knowledge environments are achieved using small robots with small hardware capabilities. To perform formation, localization, orientation, path planning and obstacle and collision avoidance should be accomplished. Finally, several static and dynamic strategies for polygon shape formation are implemented. For these formations minimizing the energy spent by the robots or the time for achieving the task, have been investigated. These strategies have better efficiency in completing the formation, since they use the cluster matching algorithm instead of the triangulation algorithm.
Study of Static Noise Margin and Circuit Analysis on Advanced Technology Node SRAM Devices by Nanoprobing (2013)

Abstract With further technology scaling, it becomes increasingly challenging for conventional methods of failure analysis (FA) to identify the cause of a failure. In this work, we present three case studies on the utilization of advanced nanoprobing for SRAM circuit analysis and fault identification on 20 nm technology node SRAM single bit devices. In the first 2 case studies, conventional failure analysis by passive voltage contrast (PVC) failed to identify any abnormality in the known failed bit. In the third case study, an abnormally bright PVC was observed by PVC inspection. In all three case studies, static noise margin of the SRAM bits during hold and read operations were performed to understand the circuit behavior of the failed bit cell. Next, nanoprobing on the individual transistors were performed to determine the failing transistor within the bit and the possible cause of the failure. TEM analysis was performed to identify and verify the failure mechanism.
Decision making on detection and triage of oral mucosa lesions in community dental practices: screening decisions and referral (2014)

Three key decision points were tested: risk assessment, need for reassessment, and need for referral. A 3-week reassessment appointment was invaluable to prevent the unnecessary referral due to confounders. There is a need for a well-defined triage pathway to facilitate oral cancer screening and a methodical and consistent approach to opportunistic screening in the dental office.
Cross-Cultural Comparison Of Stigma Toward Mental And Neurological Disorders (P6.002) (2014)

OBJECTIVE: Investigate the prevalence of stigma toward neuropsychiatric illnesses and its influencing factors across different cultures. BACKGROUND: The high social and economic burden of neuropsychiatric disorders may be further compounded by stigma. A previous study in a Hispanic community evaluating prevalence and variables associated with stigma is now expanded to study and compare results with two populations in the United States. DESIGN/METHODS: One population from Nicaragua and two from Nebraska were assessed. Participants were asked to view three videos, depicting epilepsy, schizophrenia, and dystonia. Each video was followed by a short questionnaire assessing stigma. Participants were then given additional information about the patient with dystonia and the questionnaire was repeated. Statistical analysis used Exact Chi-square, McNemar test, and more complex logistic regression models. Significance was established by a p<0.05. RESULTS: 273 participants (65.9% female) from three sites: a community health center in León, Nicaragua (92 participants), OneWorld Community Health Center in Omaha, Nebraska (85 participants, predominantly Hispanic), and Clarkson West Family Medicine Clinic in Omaha, Nebraska (96 participants, mostly non-Hispanic). Many variables were assessed including age, gender, location, level of education, and ethnic background. The results showed a complex relationship between these variables and level of stigma. Prevalence of stigma was alarming, with 50-to-90% of responses showing some degree of prejudice against neuropsychiatric disorders. Overall, significant differences existed between the three populations, with only minor differences between various ages and genders. Learning more about the people in the videos decreased stigma (p<0.01), a proof that unjustified preliminary harsh judgment is common. CONCLUSIONS: Stigma toward neuropsychiatric disorders is alarmingly common across all three communities studied. Age, gender, and level of education did not correspond to differences in prejudice, underlying the complexity of this problem. More studies are needed to evaluate the true implications of stigma toward neuropsychiatric diseases. Study Supported by: Carole Davis Memorial Fund
In situ fabrication of radiopaque microcapsules for oral delivery and real-time gastrointestinal tracking of <em>Bifidobacterium</em> (2018)

The radiopaque CA/BaSO<sub>4</sub> microcapsules provide a novel platform for efficient protection, non-invasive real-time monitoring and intestinal-targeted <i>Bifidobacterium</i> delivery.
Association of Cardiac Injury and Malignant Left Ventricular Hypertrophy With Risk of Heart Failure in African Americans (2018)

The combination of LVH and subclinical myocardial injury identifies a malignant, preclinical HF phenotype in African Americans with a very high risk of HF, particularly among men. This finding could have implications for future screening strategies that are designed to prevent HF in the population.
Hydrophobic Outer Membrane Pores Boost Testosterone Hydroxylation by Cytochrome P450 BM3 Containing Cells (2022)

The implementation of biocatalytic steroid hydroxylation processes at an industrial scale still suffers from low conversion rates. In this study, we selected variants of the self-sufficient cytochrome P450 monooxygenase BM3 from Bacillus megaterium (BM3) for the hydroxylation of testosterone either at the 2β- or 15β-position. Recombinant Escherichia coli cells were used as biocatalysts to provide a protective environment for recombinant enzymes and to ensure continuous cofactor recycling via glucose catabolism. However, only low initial whole-cell testosterone conversion rates were observed for resting cells. Results obtained with different biocatalyst formats (permeabilized cells, cell-free extracts, whole cells) indicated a limitation in substrate uptake, most likely due to the hydrophilic character of the outer membrane of E. coli . Thus, we co-expressed nine genes encoding hydrophobic outer membrane proteins potentially facilitating steroid uptake. Indeed, the application of four candidates led to increased initial testosterone hydroxylation rates. Respective whole-cell biocatalysts even exceeded activities obtained with permeabilized cells or cell-free extracts. The highest activity of 34 U g CDW −1 was obtained for a strain containing the hydrophobic outer membrane protein AlkL from Pseudomonas putida GPo1 and the BM3 variant KSA14m. Overall, we show that the straightforward application of hydrophobic outer membrane pores can boost whole-cell steroid conversion rates and thus be game-changing with regard to industrial steroid production efficiency.
A capillary electrophoresis and off-line capillary electrophoresis/electrospray ionization-quadrupole time of flight-tandem mass spectrometry approach for ganglioside analysis (2002)

A systematic study for the optimization and implementation of high-performance capillary electrophoresis (HPCE) in conjunction with negative ion electrospray ionization-quadrupole time of flight-tandem mass spectrometry (ESI-QTOF-MS/MS) for the analysis of complex glycolipids is described. The performance of the capillary electrophoresis (CE) and off-line CE/ESI-QTOF-MS approach has been explored for screening a complex ganglioside mixture from bovine brain. All instrumental and solution parameters demonstrated to require special adjustment and to have the most substantial effect on the CE separation, abundance of product ions produced in a low-energy collision-induced dissociation (CID) process and their detection by MS/MS, when attempting to identify and sequence single ganglioside molecular species from CE eluted fractions. Upon optimization of the experimental parameters, an efficient methodology emerged providing the general basic requirements for combined CE/ESI-MS analysis of this type of complex glycoconjugate.
Characterisation of Residual Stresses in Machined Surfaces of a High Strength Nickel-Base Superalloy (2006)

The near surface residual stresses introduced by turning on a nickel-base superalloy RR1000 are studied. X-ray diffraction residual stress measurements have been made in both radial and circumferential directions as a function of depth. These show systematic changes in stress magnitude and depth profile. The extent of the plastic deformation has been determined by the variation of the diffraction peak width in the XRD measurement. Both the residual stresses and the plastic work have been found to vary sharply over the first 100 mu m. The variation in unstressed lattice spacing with depth points to a heat affected zone of 40 mu m in thickness.
Radionuclide Imaging of Soft Tissue Masses with Tc-99m DTPA (1991)

A scintigraphic study was carried out on 48 patients presenting with palpable soft tissue masses. Imaging was carried out using Tc-99m DTPA in three phases (dynamic, blood pool after 5 minutes, followed by late scans after 2 hours). The resultant uptake of the agent was categorized as consistently positive (14 cases), initially positive but progressively negative (7 cases), initially negative but progressively positive (7 cases), and consistently negative (20 cases). Histopathologic examinations were carried out for all cases following biopsy. A variety of malignant and benign masses were found to localize DTPA, whereas all masses that did not concentrate the agent were proven to be lipomas. In order to determine whether the uptake of DTPA bore any relationship to blood flow, additional studies using Tc-99m labeled red cells were carried out on 15 patients with soft tissue tumors. There was no correlation between blood flow or pooling and the degree of Tc-99m DTPA uptake by the palpable masses. The sensitivity of DTPA uptake as indicative of nonlipomatous tissue was 100%, and its specificity was 91%. The predictive probability that a lesion was a liopoma if there was no DTPA uptake at any phase was 100%.
The Basal Ganglia and Posture. (1968)

The pervasive "scientism" of our time has nowhere been more evident than in the study of extrapyramidal disorders and particularly in the numerous attempts to measure and define tremor and rigidity. In recent years highly sophisticated electronic instrumentation and mathematical techniques of analysis have been brought to bear in these endeavors giving them the appearance of important scientific enterprises. However, astonishingly little has been achieved and it may fairly be said that a century of tremorology has thrown very little light on the mechanism of tremor and still less on the nature or pathophysiology of extrapyramidal disorders. Nevertheless uncritical faith in the magical powers of technic continues undiminished and the "glorious entertainment" goes on with unabated vigor. In these circumstances, this brief monograph is a most welcome and refreshing breath of fresh air demonstrating again the continuing value of astute observation and thoughtful analysis of clinical phenomena seen at the
Nonconserved charged residues of the AE2 transmembrane domain alter regulation of anion exchange by pH (2007)

We have investigated the molecular basis for regulation of the ubiquitous AE2/SLC4A2 anion exchanger by intracellular pH (pH i ) and extracellular pH (pH o ) through mutagenesis of C‐terminal transmembrane domain (TMD) amino acid residues not conserved in the closely related but pH‐insensitive AE1/SLC4A1. Selected conserved residues were also studied. AE2‐mediated Cl − /Cl − exchange was measured as DIDS‐sensitive 36 Cl − efflux from Xenopus oocytes by varying pH i at constant pH o , and by varying pH o at near‐constant pH i . Mutation of all 26 non‐conserved charged residues of the AE2 TMD yielded functional protein, but mutations of 4 conserved charged residues reduced or abolished function. Wt pH i ‐sensitivity of anion exchange was reduced upon individual mutation of AE2 TMD residues R921, F922, P1077 and R1107, whereas TMD mutants K1153R, R1155K, R1202L displayed enhanced sensitivity to acidic pH i . In addition, individual mutagenesis of non‐conserved AE2 TMD residues E981, K982 and D1075 to the corresponding AE1 residues significantly acid‐shifted pH o ‐sensitivity. These results demonstrate that multiple conserved charged residues are important for basal transport function of AE2. They further suggests that multiple non‐contiguous TMD amino acid residues contribute to regulation of AE2 by pH, and highlight the complexity of the molecular mechanisms by which pH regulates bicarbonate transporters.
A solution looking for lots of problems (2011)

Science gateways have dramatically simplified the work required by science communities to run their codes on TeraGrid resources. Gateway development typically spans the duration of a particular grant, with the first production runs occurring some months after the award and concluding near the end of the project. Scientists use gateways as a means to interface with large resources. Our gateway infrastructure facilitates this by hiding away the various details of the underlying resources and presents an intuitive way to interact with the resource. In this paper, we present our work on GPSI, a general-purpose science gateway infrastructure that can be easily customized to meet the needs of an application. This reduces the time to deployment and improves scientific productivity. Our contribution in this paper is two-fold: to elaborate our vision for a user-driven gateway infrastructure that includes components required by multiple science domains, thus aiding the speedy development of gateways, and presenting our experience in moving from our initial portal implementations to the current effort based on Python [15] and Django [16].
First update of the International Xenotransplantation Association consensus statement on conditions for undertaking clinical trials of porcine islet products in type 1 diabetes—Chapter 2b: genetically modified source pigs (2016)

Genetic modification of the source pig offers the opportunity to improve the engraftment and survival of islet xenografts. The type of modification can be tailored to the transplant setting; for example, intraportal islet xenografts have been shown to benefit from the expression of anticoagulant and anti-inflammatory transgenes, whereas cytoprotective transgenes are probably more relevant for encapsulated islets. The rapid development of pig genetic engineering, particularly with the introduction of genome editing techniques such as CRISPR-Cas, has accelerated the generation of new pig lines with multiple modifications. With pre-clinical testing in progress, it is an opportune time to consider any implications of genetic modification for the conditions for undertaking clinical trials. Obviously, the stringent requirements to fulfill designated pathogen-free status that are applied to wild-type pigs will apply equally to genetically modified (GM) source pigs. In addition, it is important from a safety perspective that the genetic modifications are characterized at the molecular level (e.g., integration site, absence of off-target mutations), the phenotypic level (e.g., durability and stability of transgene expression), and the functional level (e.g., protection of islets in vitro or in vivo, absence of detrimental effects on insulin secretion). The assessment of clinical trial protocols using GM pig islets will need to be performed on a case-by-case basis, taking into account a range of factors including the particular genetic modification(s) and the site and method of delivery.
Graph Convolutional Auto-encoder with Bi-decoder and Adaptive-sharing Adjacency. (2020)

Graph autoencoders (GAEs) are the effective unsupervised learning frameworks to learn the latent representations of graph data for network embedding. Most exiting GAE approaches typically focus on the graph reconstruction but neglect the node features reconstruction, which often results in overfitting due to the capacity of the autoencoders. Additionally, the adjacency matrix of these methods cannot accurately represent the connections among nodes in latent space when the prior information is contaminated. To address these problems, we propose a novel Graph Convolutional Auto-encoder with Bi-decoder and Adaptive-sharing Adjacency method, namely BAGE. The framework encodes the graph construction and node features into latent representations, upon which the bi-decoder is trained to reconstruct the graph construction and node features simultaneously. Moreover, the convolutional adjacency matrix is shared with the embedded graph optimization and can be adaptively learned by constructing the Laplacian, leading to more accurate connections. Consequently, the proposed method can be applied to more general datasets than the existing GAEs, i.e., data without a pre-given graph construction to prevent the GAEs from excessive dependence on the prior adjacency information. Experimental results validate the superiority of our method to the state-of-the-art network embedding methods.
Effective compressive strength of strut in CFRP-strengthened reinforced concrete deep beams following ACI 318-11 (2014)

Strut-and-tie model (STM) has been recommended by many codes and standards as a rational model for discontinuity regions in structural members. STM has been adopted in ACI building code for analysis of reinforced concrete (RC) deep beams since 2002. However, STM recommended by ACI 318-11 is only applicable for analysis of ordinary RC deep beams. This paper aims to develop the STM for CFRP strengthened RC deep beams through the strut effectiveness factor recommended by ACI 318-11. Two sets of RC deep beams were cast and tested in this research. Each set consisted of six simply-supported specimens loaded in four-point bending. The first set had no CFRP strengthening while the second was strengthened by means of CFRP sheets using two-side wet lay-up system. Each set consisted of six RC deep beams with shear span to effective depth ratio of 0.75, 1.00, 1.25, 1.50, 1.75, and 2.00.The value of strut effectiveness factor recommended by ACI 318-11 is modified using a proposed empirical relationship in this research. The empirical relationship is established based on shear span to effective depth ratio.
Acidophilic behaviour of the malolactic bacterium Oenococcus oeni (2002)

Le developpement de la bacterie lactique Œnococcus oeni est recherche en vinification pour realiser la fermentation malolactique. Dans de nombreux vins, l'acidite est un des facteurs determinants limitant la croissance de la bacterie. La presence de concentrations importantes d'ethanol et de dioxyde de soufre libre accentue cet effet deletere du milieu. La tolerance de O. oeni au pH acide fait intervenir divers mecanismes. Le premier se situe au niveau de la membrane cytoplasmique. Des les pH acides subletaux, une regulation de la fluidite membranaire est mise en place afin de controler les echanges avec le milieu exterieur. Cette modulation fait intervenir un changement de la composition membranaire et vraisemblablement la synthese de proteines de stress. Les activites enzymatiques sont egalement preservees (permeases) et d'autres se trouvent activees pour reguler le flux de protons (H + -ATPase). L'activite malolactique participe aussi a l'homeostasie du pH intracellulaire par la consommation de protons. Un couplage entre H + -ATPase et le systeme malolactique a ete mis en evidence lors de la caracterisation de mutants deficients en activite ATPasique.