Miracle-dz/UniFAR-FTUs huggingface dataset:
Domino liver transplantation in maple syrup urine disease

Liver transplantation has been reported in a few cases of maple syrup urine disease (MSUD), but is controversial. Many patients with approved indications for liver transplantation die before grafts are available. A 25‐yr‐old man with MSUD underwent liver transplantation, and his liver was used as a domino graft for a 53‐yr‐old man with hepatocellular carcinoma who had low priority on the liver transplant waiting list and was unlikely to survive until routine organ procurement. Both transplants were performed as “piggy back” procedures, reconstructing the domino graft with caval segments from the cadaveric donor. Neither required veno‐venous bypass. Whole body leucine oxidation was estimated by 13CO2 in breath after oral boluses of L‐[1‐13C]‐leucine, before and after transplantation in both patients and a control subject. The surgical outcome was successful. The patient with MSUD had marked decreases in plasma branched‐chain amino acids (BCAAs) and alloisoleucine (from 255 ± 66 to 16 ± 7 μmol/L), despite advancement of dietary protein from 6 to >40 gm/day. The domino recipient maintained near‐normal levels of plasma amino acids with no detectable alloisoleucine on unrestricted diet. Leucine oxidation increased in the patient with MSUD (from 2.2 to 5.6% recovered in 4 hours) and decreased in the recipient (from 9.7 to 6.2%). Neither patient demonstrated any apparent symptoms of MSUD over more than 7 months. In conclusion, liver transplantation substantially corrects whole body BCAA metabolism in MSUD and greatly attenuates the disease. Livers from patients with MSUD may be considered as domino grafts for patients who might otherwise not survive until transplantation. Liver Transpl 12:876–882, 2006. © 2006 AASLD.
ATTRACT: Protein–protein docking in CAPRI using a reduced protein model

Protein–protein complex structures have been predicted for CAPRI Rounds 3 and 5 using a reduced protein model. Proteins are represented by up to 3 pseudoatoms per amino acid. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to another protein. The reduced protein model allows one to perform systematic docking minimization of many thousand start structures in reasonable computer time. Flexibility of critical surface side‐chains can be accounted for by a multiple conformational copy approach. The multicopy approach allows simultaneous adjustment of side‐chain conformations and optimization of translational and rotational degrees of freedom of one protein with respect to the partner during docking. For 3 (Targets 8, 14, and 19) out of 5 CAPRI targets, the approach resulted in predictions in close agreement with experiment [root‐mean‐square deviation (RMSD) of backbone atoms within 10 Å of the protein–protein interface < 1.8 Å]. The comparison of predicted and experimental structures of the CAPRI targets indicates that besides local conformational changes (e.g., changes in side‐chain conformations), global conformational changes of the protein backbone can be critical for complex formation. These conformational changes not accounted for during docking are a likely reason for the unrealistic predictions in 2 cases (Targets 9 and 18). Proteins 2005;60:252–256. © 2005 Wiley‐Liss, Inc.
TORCH Computational Reference Kernels - A Testbed for Computer Science Research

For decades, computer scientists have sought guidance on how to evolve architectures, languages, and programming models in order to improve application performance, efficiency, and productivity. Unfortunately, without overarching advice about future directions in these areas, individual guidance is inferred from the existing software/hardware ecosystem, and each discipline often conducts their research independently assuming all other technologies remain fixed. In today's rapidly evolving world of on-chip parallelism, isolated and iterative improvements to performance may miss superior solutions in the same way gradient descent optimization techniques may get stuck in local minima. To combat this, we present TORCH: A Testbed for Optimization ResearCH. These computational reference kernels define the core problems of interest in scientific computing without mandating a specific language, algorithm, programming model, or implementation. To compliment the kernel (problem) definitions, we provide a set of algorithmically-expressed verification tests that can be used to verify a hardware/software co-designed solution produces an acceptable answer. Finally, to provide some illumination as to how researchers have implemented solutions to these problems in the past, we provide a set of reference implementations in C and MATLAB.
Patterns of Assemblage Structure Indicate a Broader Conservation Potential of Focal Amphibians for Pond Management

Small freshwater ponds host diverse and vulnerable biotic assemblages but relatively few conspicuous, specially protected taxa. In Europe, the amphibians Triturus cristatus and Pelobates fuscus are among a few species whose populations have been successfully restored using pond restoration and management activities at the landscape scale. In this study, we explored whether the ponds constructed for those two target species have wider conservation significance, particularly for other species of conservation concern. We recorded the occurrence of amphibians and selected aquatic macro-invertebrates (dragonflies; damselflies; diving beetles; water scavenger beetles) in 66 ponds specially constructed for amphibians (up to 8 years post construction) and, for comparison, in 100 man-made ponds (created by local people for cattle or garden watering, peat excavation, etc.) and 65 natural ponds in Estonia. We analysed nestedness of the species assemblages and its dependence on the environment, and described the co-occurrence patterns between the target amphibians and other aquatic species. The assemblages in all ponds were significantly nested, but the environmental determinants of nestedness and co-occurrence of particular species differed among pond types. Constructed ponds were most species-rich irrespective of the presence of the target species; however, T. cristatus was frequent in those ponds and rare elsewhere, and it showed nested patterns in every type of pond. We thus conclude that pond construction for the protected amphibians can serve broader habitat conservation aims in the short term. However, the heterogeneity and inconsistent presence of species of conservation concern observed in other types of ponds implies that long-term perspectives on pond management require more explicit consideration of different habitat and biodiversity values. We also highlight nestedness analysis as a tool that can be used for the practical task of selecting focal species for habitat conservation.
Using Data Mining for Discovering Patterns in Autonomic Storage Systems

In order to be self-tuning, self-managing, self-healing and selfprotecting, a storage system needs to be able to automatically characterize access patterns. This paper proposes an approach that uses data mining techniques to systematically mine access sequences in a storage system to characterize storage behaviors. More specifically, we use frequent sequence mining algorithms to find block access correlations which can be used to improve the effectiveness of subsystems such as storage caching and disk scheduling, and for disk power management. This paper reports our preliminary results of discovering block correlations from storage access sequences using a recently proposed data mining algorithm called CloSpan.
Two-stage opportunistic interference alignment for downlink MU-MIMO cellular systems

In this paper, a two-stage opportunistic interference alignment (OIA) algorithm is proposed for the downlink multi-cell multi-user multiple-input-multiple-output (MU-MIMO) system. Two precoders/postcoders are used at each transmitter/receiver respectively to combat interference. The inner precoder/postcoder pair are used to cancel out the inter-cell interference (ICI) using perfect IA approach, while the outer precoder/postcoder pair are used to minimize the intra-cell or the inter-user interference (IUI) using rank constrained rank minimization (RCRM) based IA approach. According to the limited spatial resources at base stations (BSs), in the second stage, users at which the sum interference span the lowest dimensions are selected by each BS. The proposed algorithm is compared with different downlink OIA algorithms from literature in terms of the average sum rate and the average achieved number of degrees of freedom (DoFs). Simulations show that the proposed algorithm achieves higher sum rate specially at high signal-to-noise ratios (SNRs). Moreover, the proposed algorithm achieves higher number of streams/user compared to other algorithms.
Velocity Integration in a Multilayer Neural Field Model of Spatial Working Memory

We analyze a multilayer neural field model of spatial working memory, focusing on the impact of interlaminar connectivity, spatial heterogeneity, and velocity inputs. Models of spatial working memory typically employ networks that generate persistent activity via a combination of local excitation and lateral inhibition. Our model comprises a multilayer set of equations that describes connectivity between neurons in the same and different layers using an integral term. The kernel of this integral term then captures the impact of different interlaminar connection strengths, spatial heterogeneity, and velocity input. We begin our analysis by focusing on how interlaminar connectivity shapes the form and stability of (persistent) bump attractor solutions to the model. Subsequently, we derive a low-dimensional approximation that describes how spatial heterogeneity, velocity input, and noise combine to determine the position of bump solutions. The main impact of spatial heterogeneity is to break the translation .
Research News

In this section we invite researchers to share news of projects they are involved with, or which they have recently completed, and their views on research more generally. We hope, in this way, that Research News will provide a useful alternative avenue for dissemination of research  ndings, to support the networking of ideas in the  eld of school leadership and management, stimulate meaningful debate, and encourage the further use of educational research  ndings by practitioners. In keeping with the Journal’s focus we are interested in empirical research in different education systems, from the UK and elsewhere, that contributes to our understanding of school leadership and management. Contributions may relate to fully-funded research, studies undertaken by practitioners, or work for a doctoral degree. These might include reports of new grants awarded, studies in progress, summaries of  ndings, lists of publications from projects,  nal reports, requests for assistance, topical ‘thought’ pieces, descriptions of new methods, and unpublished conference reports. If appropriate, the contribution should indicate the project title, timespan, aims, and contact details. Once accepted for publication, reports can be published in Research News within three months. Please send your contributions, preferably via E-mail, to the editor of this section: Neil Selwyn, School of Social Sciences, Cardiff University, Glamorgan Building, King Edward VII Avenue, Cardiff, CF10 3WT, UK. E-mail: selwynnc@cardiff. ac.uk
Effect of weight loss , exercise , or both on cognition and quality of life in obese older adults 1 – 4

Background: Obesity impairs cognition and health-related quality of life (HRQOL) in older adults; however, the appropriate treatment of obese older adults remains controversial. Objective: The objective was to determine the independent and combined effects of weight loss and exercise on cognition, mood, and HRQOL in obese older adults. Design: One hundred seven frail, obese older adults were randomly assigned to a control, weight-management (diet), exercise, or weight-management-plus-exercise (diet-exercise) group for 1 y. In this secondary analysis, main outcomes were Modified MiniMental State Examination (3MS) and total Impact of Weight on Quality of Life-Lite (IWQOL) scores. Other outcomes included Word Fluency Test, Trail Making Test Parts A and B, and Geriatric Depression Scale (GDS) scores. Results: Scores on the 3MS improved more in the diet (mean6 SE: 1.7 6 0.4), exercise (2.8 6 0.4), and diet-exercise (2.9 6 0.4) groups than in the control group (0.1 6 0.4) (between-group P = 0.0001–0.04); scores in the diet-exercise group improved more than in the diet group but not more than in the exercise group. Scores on the Word Fluency Test improved more in the exercise (4.1 6 0.8) and diet-exercise (4.26 0.7) groups than in the control group (20.8 6 0.8; both P = 0.001). For the Trail Making Test Part A, scores in the diet-exercise group (211.8 6 1.9) improved more than in the control group (20.8 6 1.9) (P = 0.001); a similar finding was observed for the Trail Making Test Part B. Scores on the IWQOL improved more in the diet (7.6 6 1.6), exercise (10.1 6 1.6), and diet-exercise (14.0 6 1.4) groups than in the control group (0.3 6 1.6) (P = 0.0001–0.03); scores in the diet-exercise group improved more than in the diet group but not more than in the exercise group. In the diet-exercise group, peak oxygen consumption and strength changes were independent predictors of 3MS changes; weight and strength changes were independent predictors of IWQOL changes. GDS scores did not change. Conclusions: Weight loss and exercise each improve cognition and HRQOL, but their combination may provide benefits similar to exercise alone. These findings could inform practice guidelines with regard to optimal treatment strategies for obese older adults. This trial was registered at clinicaltrials.gov as NCT00146107. Am J Clin Nutr 2014;100:189–98.
Parle: parallelizing stochastic gradient descent

We propose a new algorithm called Parle for parallel training of deep networks that converges 2-4x faster than a data-parallel implementation of SGD, while achieving significantly improved error rates that are nearly state-of-the-art on several benchmarks including CIFAR-10 and CIFAR-100, without introducing any additional hyper-parameters. We exploit the phenomenon of flat minima that has been shown to lead to improved generalization error for deep networks. Parle requires very infrequent communication with the parameter server and instead performs more computation on each client, which makes it well-suited to both single-machine, multi-GPU settings and distributed implementations.
Insect larval expression process is optimized by generating fusions with green fluorescent protein.

The insect larvae/baculovirus protein production process was dramatically simplified by expressing fusion proteins containing green fluorescent protein (GFP) and the product-of-interest. In this case, human interleukin-2 (hIL-2) and chloramphenicol acetyl-transferase (CAT) were model products. Specifically, our fusion construct was comprised of a histidine affinity ligand for simplified purification using immobilized metal affinity chromatography (IMAC), the UV-optimized GFP (GFPuv) as a marker, an enterokinase cleavage site for recovery of the product from the fusion, and the product, hIL-2 or CAT. Both the approximately 52 kDa GFPuv/hIL-2 and approximately 63 kDa GFPuv/CAT fusions were expressed in Trichoplusia ni larvae at 9.0 microg-hIL-2 and 24.1 microg-CAT per larva, respectively. The GFP enabled clear identification of the infection process, harvest time, and more importantly, the quantity of product protein. Because the GFP served as a marker, this technique obviates the need for in-process Western analyses (during expression, separation, and purification stages). As a purification marker, GFP facilitated rapid identification of product-containing elution fractions (Cha et al., 1999b), as well as product-containing waste fractions (e.g., cell pellet). Also, because the fluorescence intensity was linear with hIL-2 and CAT, we were able to select the highest-producing larvae. That is, three fold more product was found in the brightest larva compared to the average. Finally, because the GFP is attached to the product protein and the producing larvae can be selected, the infection and production processes can be made semi-continuous or continuous, replacing the current batch process. These advantages should help to enable commercialization of larvae as expression hosts.
Transdifferentiation of hepatocyte‐like cells from the human hepatoma HepaRG cell line through bipotent progenitor

Hepatic tumors, exhibiting mature hepatocytes and undifferentiated cells merging with cholangiocyte and hepatocyte phenotypes, are frequently described. The mechanisms by which they occur remain unclear. We report differentiation and transdifferentiation behaviors of human HepaRG cells isolated from a differentiated tumor developed consecutively to chronic HCV infection. We demonstrate that, in vitro, proliferating HepaRG cells differentiate toward hepatocyte‐like and biliary‐like cells at confluence. If hepatocyte‐like cells are selectively isolated and cultured at high cell density, they proliferate and preserve their differentiation status. However, when plated at low density, they transdifferentiate into hepatocytic and biliary lineages through a bipotent progenitor. In accordance, transplantation of either undifferentiated or differentiated HepaRG cells in uPA/SCID mouse damaged liver gives rise mainly to functional human hepatocytes infiltrating mouse parenchyma. Analysis of the differentiation/transdifferentiation process reveals that: (1) the reversible differentiation fate of HepaRG cells is related to the absence of p21CIP1 and p53 accumulation in differentiated cells; (2) HepaRG bipotent progenitors express the main markers of in vivo hepatic progenitors, and that cell differentiation process is linked to loss of their expression; (3) early and transient changes of β‐catenin localization and HNF3β expression are correlated to Notch3 upregulation during hepatobiliary commitment of HepaRG cells. Conclusion: Our results demonstrate the great plasticity of transformed hepatic progenitor cells and suggest that the transdifferentiation process could supply the pool of hepatic progenitor cells. Moreover, they highlight possible mechanisms by which transdifferentiation and proliferation of unipotent hepatocytes might cooperate in the development of mixed and differentiated tumors. (HEPATOLOGY 2007;45:957–967.)
PowerFactorization : 3D reconstruction with missing or uncertain data

Many problems in computer vision may be considered as low-rank approximation problems, in which a matrix of measured data must be approximated by a matrix of given low rank. If the matrix has no missing entries, then this is easily accomplished by a Singular Value Decomposition (SVD). If some measurements are missing however, and the matrix has holes, then the SVD method can not be applied. We present here a practical iterative method for approximating a data matrix, possibly with missing entries, with another matrix of small rank r. For a complete data matrix the method reduces to the well-known ”Power Method” which is provably convergent to a unique global optimum. If the data is well approximated by a matrix of rank r the Power Method has rapid convergence. Our method for incomplete data is applied to several problems of 3D reconstruction, generalizing the Tomasi-Kanade method for orthographic cameras and the Sturm-Triggs method for projective cameras to missing and uncertain data.
Putting Test Results to Work

"There is ample evidence that children's reading abilities are frequently tested . ; there is less evidence that the results of testing are used effectively" (1). This is one of the most startling conclusions that Austin and Morrison report in their book The First R. How can the classroom teacher use test results to the best advantage? Classroom testing has two purposes: to diagnose pupils' needs and to use the results to provide a reading program based on those needs. Apparently, the second purpose is not getting the attention it deserves. One major problem the teacher faces in diagnosing needs is test selection. Standardized group tests in reading overestimate pupil performance. For this reason they are often disregarded by classroom teachers who rely entirely on informal measures to determine instructional needs. The limitations of informal measures have often been cited-lack of validity, lack of reliability, and fragmentation of skill-measurement. Because of these limitations, some classroom teachers hesitate to construct and use informal reading inventories. The study reported here was designed to evaluate the contributions that reading measurements-standardized and informal-make to classroom grouping for instruction. In the study, informal as well as standardized instruments were used. The study was conducted at the Campus School of State University College at Fredonia, New York. The children were fifth-graders-twentyfive in all-whose intelligence quotients ranged from 97 to 135. All the pupils came from families in the middleor upper-middle class. More than 60 per cent of the pupils came from homes in which one or both parents had attended or graduated from college. The reading program for the children at the Campus School had included work in various basal reader series as well as guided independent reading activities. Before the study, classroom grouping was based on information obtained from each pupil's cumulative folder. Twenty pupils were working with reading materials at grade level; five pupils were working
CrowDM: the System for Collaborative Platform Data Analysis

The paper considers a data analysis system of the Witology company collaborative platform and mainly describes a methodology and results of the rst experiments. The developed system is based on several models and methods of modern analysis of object-attribute and unstructured data (texts) such as Formal Concept Analysis, multimodal clustering, association rules mining and keywords and collocations extraction from texts.
Self-Expression and Depressive Symptoms in Late Life

The purpose of this study was to develop and test a latent-variable model to assess the relationship between self-expression and depressive symptoms in late life. Data from a nationwide survey of older adults (n = 1,013) provided empirical support for the following theoretical linkages embedded in this conceptual framework: (1) Higher levels of educational attainment are associated with greater self-expression, (2) older people who find avenues for self-expression are more likely to develop senses of meaning in life, (3) older adults who find senses of meaning in life are more likely to feel grateful, and (4) elders who feel grateful are less likely to experience symptoms of depression.