gebhart/patrepeval huggingface dataset:
Current status of diagnosis and treatment of lysosomal storage diseases in China (2006)

Lysosomal storage diseases (LSDs) are a group of inherited disorders caused by deficiency of lysosomal enzymes or structural components. LSDs have been models of molecular and cellular therapies for inherited metabolic diseases. Enzyme replacement therapy (ERT), bone marrow transplantation and substrate reduction therapy (SRT) have been shown to be effective for many of the LSDs. Early diagnosis and treatment have best chance for a positive outcome. We reviewed the case reports, diagnosis and treatment of LSDs in China. World J Pediatr 2006;4:245-251
Interactor-Guided Dephosphorylation by Protein Phosphatase-1 (2013)

Protein phosphatase-1 (PP1) is an essential enzyme for every eukaryotic cell and catalyzes more than half of all protein dephosphorylations at serine and threonine residues. The free catalytic subunit of PP1 shows little substrate selectivity but is tightly regulated in vivo by a large variety of structurally unrelated PP1-interacting proteins (PIPs). PIPs form highly specific dimeric or trimeric PP1 holoenzymes by acting as substrates, inhibitors, and/or substrate-specifiers. The surface of PP1 contains many binding sites for short PP1-docking motifs that are combined by PIPs to create a PP1-binding code that is universal, specific, degenerate, nonexclusive, and dynamic. These properties of the PP1-binding code can be used for the rational design of small molecules that disrupt subsets of PP1 holoenzymes and have a therapeutic potential.
Progressive Face Super-Resolution via Attention to Facial Landmark. (2019)

Face Super-Resolution (SR) is a subfield of the SR domain that specifically targets the reconstruction of face images. The main challenge of face SR is to restore essential facial features without distortion. We propose a novel face SR method that generates photo-realistic 8x super-resolved face images with fully retained facial details. To that end, we adopt a progressive training method, which allows stable training by splitting the network into successive steps, each producing output with a progressively higher resolution. We also propose a novel facial attention loss and apply it at each step to focus on restoring facial attributes in greater details by multiplying the pixel difference and heatmap values. Lastly, we propose a compressed version of the state-of-the-art face alignment network (FAN) for landmark heatmap extraction. With the proposed FAN, we can extract the heatmaps suitable for face SR and also reduce the overall training time. Experimental results verify that our method outperforms state-of-the-art methods in both qualitative and quantitative measurements, especially in perceptual quality.
Function and structure of heterodimeric amino acid transporters (2001)

Heterodimeric amino acid transporters are comprised of two subunits, a polytopic membrane protein (light chain) and an associated type II membrane protein (heavy chain). The heavy chain rbAT (related to b(0,+) amino acid transporter) associates with the light chain b(0,+)AT (b(0,+) amino acid transporter) to form the amino acid transport system b(0,+), whereas the homologous heavy chain 4F2hc interacts with several light chains to form system L (with LAT1 and LAT2), system y(+)L (with y(+)LAT1 and y(+)LAT2), system x (with xAT), or system asc (with asc1). The association of light chains with the two heavy chains is not unambiguous. rbAT may interact with LAT2 and y(+)LAT1 and vice versa; 4F2hc may interact with b(0,+)AT when overexpressed. 4F2hc is necessary for trafficking of the light chain to the plasma membrane, whereas the light chains are thought to determine the transport characteristics of the respective heterodimer. In contrast to 4F2hc, mutations in rbAT suggest that rbAT itself takes part in the transport besides serving for the trafficking of the light chain to the cell surface. Heavy and light subunits are linked together by a disulfide bridge. The disulfide bridge, however, is not necessary for the trafficking of rbAT or 4F2 heterodimers to the membrane or for the functioning of the transporter. However, there is experimental evidence that the disulfide bridge in the 4F2hc/LAT1 heterodimer plays a role in the regulation of a cation channel. These results highlight complex interactions between the different subunits of heterodimeric amino acid transporters and suggest that despite high grades of homology, the interactions between rbAT and 4F2hc and their respective partners may be different.
Structural Properties of Stochastic Dynamic Programs (2002)

In Markov models of sequential decision processes, one is often interested in showing that the value function is monotonic, convex, and/or supermodular in the state variables. These kinds of results can be used to develop a qualitative understanding of the model and characterize how the results will change with changes in model parameters. In this paper we present several fundamental results for establishing these kinds of properties. The results are, in essence, "metatheorems" showing that the value functions satisfy property P if the reward functions satisfy property P and the transition probabilities satisfy a stochastic version of this property. We focus our attention on closed convex cone properties, a large class of properties that includes monotonicity, convexity, and supermodularity, as well as combinations of these and many other properties of interest.
Content adaptive gop size control with feedback channel suppression in distributed video coding (2009)

This paper presents a novel algorithm for content adaptive GOP size control in distributed video coding. The GOP size is dynamically varied along the sequence, depending on motion activity. Automatic mode selection allows the system to switch between H.264 intra-coding and Wyner-Ziv coding modes to optimize the overall performance. Furthermore, the encoder determines a suitable compression ratio for the Wyner-Ziv frames without the need for a feedback channel. Simulation results show significant improvement in the average system performance, compared to fixed GOP Wyner-Ziv and H.264 intra-coding.
Automatic Chord Detection Incorporating Beat and Key Detection (2007)

We introduce an algorithm that analyzes audio signals to extract chord-sequence information. The main goal of our approach lies in incorporating music theoretical knowledge without restricting the input data to a narrow range of musical styles. At the basis of our approach lies pitch detection using enhanced autocorrelation, supported by key detection and beat tracking. The chords themselves are identified by comparing generated and reference pitch class profiles. A smoothing algorithm is applied to the chord sequence which optimizes the number of chord changes and thus takes into consideration the comparatively stable nature of chords. In this paper we present an evaluation performed on a large set of 35 pieces of diverse music showing an average performance of 65% accuracy.
GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations (2013)

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
A family of multifunctional thiamine-repressible expression vectors for fission yeast (2000)

A series of thiamine-repressible shuttle vectors has been constructed to allow a more efficient DNA manipulation in Schizosaccharomyces pombe. These high-copy-number vectors with regulatable expression (pJR) are based on the backbone of the pREP-3X, pREP-41X and pREP-81X plasmids. The pJR vectors are all uniform in structure, containing: (a) sequences for replication (ori) and selection (AmpR) in Escherichia coli; (b) the f1 ori sequence of the phage f1 for packaging of ssDNA, making them suitable for site-directed mutagenesis; and (c) the ars1 sequence for replication in S. pombe. The pJR vectors differ among them in: (a) the selectable marker (Saccharomyces cerevisiae LEU 2 gene, which complements S. pombe leu1- gene and S. pombe ura4+ and his3+ genes); (b) the thiamine-repressible nmt1 promoter (3X, 41X and 81X with extremely high, moderate or low transcription efficiency, respectively); and (c) the multiple cloning site (two multiple cloning sites, with 12 restriction sites each). The expression level of the pJR vectors has been analysed using the beta-galactosidase gene as reporter. Three levels of expression for each nmt1 promoter version, with any selectable marker and for either repressed or induced conditions, have been found. The expression is dependent on the distance to the initiation codon, varying from 0.001 to 15 times the activity characterized for the pREP plasmids. Also, the gene expression has been found to be extremely sensitive to the nucleotide sequence prior to the initiation codon, being up to 50-fold higher with an A/T sequence than with a G/C sequence. Finally, the beta-galactosidase mRNA levels were found to be similar in each nmt1 series, suggesting a translational effect on gene expression. As a result, any of these 18 new vectors allow performing gene expression in fission yeast, as well as a more versatile cloning, sequencing and mutagenesis, directly in the plasmid without the need for subcloning into intermediary vectors.
Antibiotic prescribing for upper respiratory infections: European primary paediatricians’ knowledge, attitudes and practice (2012)

There is a clear need for an educational intervention focused on European primary care paediatricians based on the risk-benefit analysis associated with the antibiotic prescribing for minor URIs, to reduce inappropriate prescribing.
Transboundary and Emerging Diseases (2023)

Duck Tembusu virus (DTMUV) is an emerging avian pathogenic flavivirus that causes neurological disorders and acute egg drop syndrome in ducks. Multiple genotypes of DTMUV, including clusters 1, 2, and 3, have been identified, and recent evidence suggests a correlation between viral genotype and disease severity. Our recent study demonstrated that DTMUV cluster 2.1 induces more severe clinical disease in ducks than cluster 1; however, the underlying mechanisms responsible for this difference remain unclear. Macrophages are key target cells for DTMUV replication and play a crucial role during the early stage of viral pathogenesis. Therefore, we hypothesized that distinct DTMUV genotypes may differentially regulate macrophage apoptosis, thereby influencing viral replication and modulating T lymphocyte responses. To investigate this, we developed an in vitro protocol to generate duck monocyte-derived macrophages (MDMs) and assessed their response to infection with two different DTMUV genotypes: cluster 1 and cluster 2.1. Our results showed that DTMUV cluster 1 infection significantly increased macrophage apoptosis and reduced cell viability. In contrast, DTMUV cluster 2.1-infected MDM exhibited higher cell viability and fewer apoptotic cells. Correspondingly, viral titers in supernatants from DTMUV cluster 2.1-infected cultures were significantly higher than those from cluster 1. Furthermore, culture with DTMUV cluster 2.1 resulted in enhanced proliferation of Th (CD3+CD4+BrdU+) and cytotoxic T lymphocyte (CTL; CD3+CD8+BrdU+) lymphocytes in both naïve peripheral blood mononuclear cells (PBMCs) and macrophage-peripheral blood lymphocytes (PBLs) co-culture systems. These results suggest that the inhibition of apoptosis in DTMUV cluster 2.1-infected macrophages may enhance antigen-specific T lymphocyte responses. Overall, our findings reveal a genotype-dependent mechanism by which DTMUV modulates macrophage survival, thereby influencing both viral replication and T cell activation, and ultimately contributing to genotype-specific immunopathogenesis. These insights deepen our understanding of DTMUV immunopathogenesis and may inform the development of more effective genotype-targeted vaccination and disease control strategies.
Electrodegradation of 2,4-dichlorophenoxyacetic acid herbicide from aqueous solution using three-dimensional electrode reactor with G/β-PbO<sub>2</sub>anode: Taguchi optimization and degradation mechanism determination (2018)

This study aimed to investigate the electro-degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) from aqueous solution using two and three-dimensional electrode (2D and 3D) reactors with graphite(G)/β-PbO<sub>2</sub> anode. To increase the degradation efficiency, affecting parameters on the electro-degradation process were investigated and optimized by adopting the Taguchi design of experiments approach. The structure, morphology and electrochemical properties of the electrodes were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), linear sweep voltammetry and cyclic voltammograms. The controllable factors, <i>i.e.</i>, electrolysis time, 2,4-D initial concentration, solution pH and current density (<i>j</i>) were optimized. Under optimum conditions, the 2,4-D degradation efficiency was 75.6% using 2D and 93.5% using 3D electrode processes. The percentage contribution of each controllable factor was also determined. The pH of the solution was identified as the most influential factor, and its percentage contribution value was up to 39.9% and 40.4% for 2D and 3D electrode processes, respectively. Considering the parameters of the kinetics, it was found that the degradation of 2,4-D and removal of COD using the G/β-PbO<sub>2</sub> electrode obey the pseudo-first order kinetics. In addition, the mineralization pathway of 2,4-D at G/β-PbO<sub>2</sub> electrode was proposed. The results also demonstrated that the 3D electrode process with G/β-PbO<sub>2</sub> anode can be considered as a useful method for degradation and mineralization of 2,4-D herbicides from aqueous solution.
Ruthenium‐Catalyzed Reactions—A Treasure Trove of Atom‐Economic Transformations (2005)

The demand for new chemicals spanning the fields of health care to materials science combined with the pressure to produce these substances in an environmentally benign fashion pose great challenges to the synthetic chemical community. The maximization of synthetic efficiency by the conversion of simple building blocks into complex targets remains a fundamental goal. In this context, ruthenium complexes catalyze a number of non-metathesis conversions and allow the rapid assembly of complex molecules with high selectivity and atom economy. These complexes often exhibit unusual reactivity. Careful consideration of the mechanistic underpinnings of the transformations can lead to the design of new reactions and the discovery of new reactivity.
Surface-wave tomography to resolve water table: Almond Orchard case study, Modesto, California (2017)

We are investigating the potential of using seismic surface waves to image the first 20m in an Almond Orchard. The objective is to measure changes in water table levels. Seismic shear waves are known to be sensitive to shear wave velocity in the near surface (Socco et al., 2010), so the Rayleigh waves should provide a detection tool for monitoring groundwater infiltration experiments. In December 2016 we acquired basline data at an almond orchard near Modesto, CA using a new seismic acquisition geometry for 3D surface wave analysis called TomoSW (Rector, et al, 2015). In this approach we first collect a standard MASW (Multichannel Analysis of Surface Waves) survey and estimate surface wave velocities, arrival times, and frequency content (Miller et al., 1999). Then we deploy sources and receivers in a 3D geometry such as along the sides of a rectangle (Figure 1). The Rayleigh wave arrival times for a particular narrow frequency range are measured and used in a frequency dependent 2D tomographic inversion to create phase velocity as a function of position within the rectangle. This data is then inverted for shear wave velocity versus depth. Preliminary field results show a potential depression of the water table within a portion of the survey area. Presentation Date: Tuesday, September 26, 2017 Start Time: 2:15 PM Location: 370C Presentation Type: ORAL
Pharmacological Therapy of Cushings Syndrome: Drugs and Indications (2007)

Agents that inhibit steroidogenesis are useful in all forms of Cushing's syndrome and are effective in about 70% of patients. Main indications for drug therapy include preparation for surgery, persistence or recurrence after surgery, while awaiting for the effect of radiation therapy, occult ectopic ACTH syndrome, severe hypercortisolism and malignancy related hypercortisolism.
Bacterial Vaginosis (2012)

Bacterial vaginosis (BV) is a common cause of vaginitis and represents a synergistic polymicrobial syndrome characterized by depletion of Lactobacillus species, especially those that produce hydrogen peroxide, and acquisition of complex bacterial communities that include many fastidious bacteria recently detected using PCR. BV has been associated with numerous adverse sequelae, including pelvic inflammatory disease, post-surgical infections, preterm delivery, and increases in risk of HIV infection. This chapter provides an update on prevention and management of BV.
Positive behavioural support in schools for children and adolescents with intellectual disabilities whose behaviour challenges (2016)

Decision-makers with limited budgets want to know the economic consequences of their decisions. Is there an economic case for positive behavioural support (PBS)? A small before-after study assessing the impact of PBS on challenging behaviours and positive social and communication skills in children and adolescents with intellectual disabilities and behaviours that challenge was followed by an evaluation of costs. Results were compared with the costs of alternative packages of care currently available in England obtained from a Delphi exercise conducted alongside the study. Children and adolescents supported with PBS showed improvement in challenging behaviours and social and communication skills, at a total weekly cost of GBP 1909 (and GBP 1951 including carer-related costs). PBS in schools for children and adolescents with intellectual disabilities and behaviours that challenge may help to support them in the community with potential improvements in outcomes and also cost advantages.
Variable-Inverter-Rectifier-Transformer: A Hybrid Electronic and Magnetic Structure Enabling Adjustable High Step-Down Conversion Ratios (2018)

This paper proposes a hybrid electronic and magnetic structure named a variable-inverter-rectifier-transformer (VIRT) that enables a transformer with fractional and reconfigurable effective turns ratios (e.g., 12:0.5, 12:2/3, 12:1, and 12:2). This functionality is valuable in converters with wide operating voltage ranges and high step-up/down, as it offers a means to reduce the turns count and copper loss within the transformer while also facilitating voltage doubling and quadrupling. These properties are especially beneficial for miniaturizing the transformer stage in many power electronics applications, such as universal serial bus wall chargers. We introduce the principle of operation of the structure and present models for its magnetic and electrical behavior. The instance of VIRT described in this paper comprises four half-bridge switching cells distributed around a planar magnetic core and connected to two “half-turns” wound through that core. By controlling the operating modes of the half-bridge cells, we gain control over the flux paths and current paths used in the transformer, and this hybridization enables fractional and reconfigurable effective turns ratios. An experimental prototype integrates the VIRT with a stacked-bridge <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LLC</i> converter to accommodate a widely varying input (120–380 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\text{V}_{\text{dc}}$</tex-math></inline-formula> ) and output (5–20 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\text{V}_{\text{dc}}$</tex-math></inline-formula> ), and VIRT is shown to be highly beneficial in keeping efficiency high over this wide output voltage range.
Cast polycrystalline silicon solar cell with grooved surface (2002)

Improving the efficiency of polycrystalline silicon solar cells by using an efficient surface groove structure and a thinner bulk active layer is described. The cell surface was mechanically grooved and chemically etched. A conversion efficiency of 15.5% for a 10*10 cm polycrystalline silicon cell was obtained with 1.0(%) surplus compared with the texture surface polycrystalline solar cell (reference cell: 14.5%). The grooved surface is effective for minimizing the reflectance of polycrystalline silicon solar cells. A thinner-groove polycrystalline cell of under 200 mu m substrate thickness improves the long-wavelength collection efficiency and the conversion efficiency.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Clustered Multi-Task Learning Via Alternating Structure Optimization. (2011)

Multi-task learning (MTL) learns multiple related tasks simultaneously to improve generalization performance. Alternating structure optimization (ASO) is a popular MTL method that learns a shared low-dimensional predictive structure on hypothesis spaces from multiple related tasks. It has been applied successfully in many real world applications. As an alternative MTL approach, clustered multi-task learning (CMTL) assumes that multiple tasks follow a clustered structure, i.e., tasks are partitioned into a set of groups where tasks in the same group are similar to each other, and that such a clustered structure is unknown a priori. The objectives in ASO and CMTL differ in how multiple tasks are related. Interestingly, we show in this paper the equivalence relationship between ASO and CMTL, providing significant new insights into ASO and CMTL as well as their inherent relationship. The CMTL formulation is non-convex, and we adopt a convex relaxation to the CMTL formulation. We further establish the equivalence relationship between the proposed convex relaxation of CMTL and an existing convex relaxation of ASO, and show that the proposed convex CMTL formulation is significantly more efficient especially for high-dimensional data. In addition, we present three algorithms for solving the convex CMTL formulation. We report experimental results on benchmark datasets to demonstrate the efficiency of the proposed algorithms.