Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting absolute contact numbers of native protein structure from amino acid sequence

The contact number of an amino acid residue in a protein structure is defined by the number of Cβ atoms around the Cβ atom of the given residue, a quantity similar to, but different from, solvent accessible surface area. We present a method to predict the contact numbers of a protein from its amino acid sequence. The method is based on a simple linear regression scheme and predicts the absolute values of contact numbers. When single sequences are used for both parameter estimation and cross‐validation, the present method predicts the contact numbers with a correlation coefficient of 0.555 on average. When multiple sequence alignments are used, the correlation increases to 0.627, which is a significant improvement over previous methods. In terms of discrete states prediction, the accuracies for 2‐, 3‐, and 10‐state predictions are, respectively, 71.4%, 54.1%, and 18.9% with residue type‐dependent unbiased thresholds, and 76.3%, 59.2%, and 21.8% with residue type‐independent unbiased thresholds. The difference between accessible surface area and contact number from a prediction viewpoint and the application of contact number prediction to three‐dimensional structure prediction are discussed. Proteins 2005. © 2004 Wiley‐Liss, Inc.
How Do Coupled File Changes Influence How Developers Seek Help During Maintenance Tasks?

Software repositories contain a lot of information that can be transformed into suggestions other files they need to modify during maintenance tasks (so-called "coupled changes"). Existing studies however ignore developer feedback and their influence on the developer strategy for getting help during maintenance tasks. We used the Grounded Theory approach to investigate screen capture videos from an experiment to find which information sources developers use to find help and what is their relevance. We compared the frequency as well as the sequence patterns of used information sources both for the developers using coupled change suggestions and those not using them. We found a set of information sources where the developers seek for help and identified two categories of relevance. Also, we discovered that for the tasks using coupled change suggestions, the developers used mostly the internal IDE elements as an information source whereby the developers not using coupled change suggestions often used external sources like the documentation or the web. Coupled change suggestions influence the strategy how the developers seek for help by reducing the search for information on external locations which makes the process of solving maintenance tasks more compact.
Asynchronous Binaural Spatial Audition Sensor With 2$\,\times\,$64$\,\times\,$4 Channel Output

This paper proposes an integrated event-based binaural silicon cochlea system aimed at efficient spatial audition and auditory scene analysis. The cochlea chip has a matched pair of digitally-calibrated 64-stage cascaded analog second-order filter banks with 512 pulse-frequency modulated (PFM) address-event representation (AER) outputs. The quality factors (Qs) of channels are individually adjusted by local DACs. The 2P4M 0.35 um CMOS chip consumes an average power of 14 mW including its integrated microphone preamplifiers and biasing circuits. Typical speech data rates are 10 k to 100 k events per second (eps) with peak output rates of 10 Meps. The event timing jitter is 2 us for a 250 mVpp input. It is shown that the computational cost of an event-driven source localization application can be up to 40 times lower when compared to a conventional cross-correlation approach.
Increased frequency of extremely skewed X chromosome inactivation in juvenile idiopathic arthritis.

OBJECTIVE Juvenile idiopathic arthritis (JIA) is a childhood rheumatic disease of unknown etiology. Two subgroups of JIA, i.e., oligoarticular and polyarticular, are thought to have an autoimmune component, and show a higher female:male ratio. Skewed X chromosome inactivation (XCI) has previously been shown to be associated with scleroderma and autoimmune thyroiditis, 2 autoimmune disorders occurring predominantly in females. This study was undertaken to extend the analysis to the pediatric age group and to determine the XCI profiles of patients with JIA. METHODS A polymorphic repeat in the androgen receptor gene was genotyped to determine XCI status in 81 female patients with JIA (21 with polyarticular disease and 60 with oligoarticular disease) and 211 healthy female controls. DNA obtained from venous blood samples was used for this analysis. RESULTS Informative data were obtained on 62 JIA patients and 155 controls. Skewed XCI was observed in 14 patients (22.6%) and 11 controls (7.1%) (P = 0.0036), and extreme skewing was apparent in 8 patients (12.9%) and 2 controls (1.3%) (P = 0.0008). CONCLUSION Our findings in the present study indicate that skewed XCI may be a risk factor for the occurrence of autoimmune disorders, including JIA.
Granulocyte colony-stimulating factor combined regimen in cord blood transplantation for acute myeloid leukemia: a nationwide retrospective analysis in Japan

Cord blood transplantation (CBT) from an unrelated donor has been increasingly used as an alternative transplant method for adult patients without human leukocyte antigen (HLA)-compatible related or unrelated donors. [1][1]–[4][2] However, the main disadvantage of CBT is still the limited cell dose
Business Intelligence (BI) implementation from the perspective of individual change

Change is central in the implementation of Information Technology (IT). This paper reports on a study in which the aim was to examine the nature of change at the individual level with an analysis based on interviews with representatives from a Business Intelligence (BI) solution provider and a group of clients. The implementations seemed to have occurred without great difficulty, BI learning was quick, intuitive, and the process generated a positive affect. Changes occurred in work practices, in the relationships between professionals, with regard to information, and in decision making. The study uses different theoretical approaches and proposes the application of an analytical perspective that includes affective, cognitive and behavioral aspects in order to investigate IT adoption. On a practical level, the study contributes to the knowledge regarding a particular technology - BI and, consequently, provides professionals with the opportunity to expand their knowledge of the perceptions people have of technology, which can lead to reflection and differentiated practices.
KNOWLEDGE MANAGEMENT PRACTICES OF CONSTRUCTION PROJECT MANAGERS

The construction industry delivers large, expensive, custom-built facilities at the end of a construction process. It is a strong, knowledge-based industry that relies heavily on knowledge input. As result, the concept of knowledge management (KM), which saves much time and energy and prevents “Reinventing the vehicle”, has been increasingly popular in recent years within the industry, and is being recognized to achieve higher client satisfaction, better timing & cost control and innovation. However, owing to the time constraint and cultural practice of the construction industry, capturing and transferring project knowledge have not been well achieved. Moreover, good knowledge management does not result from the implementation of sophisticated or tailor made KM tools, human factors play an important role. Meanwhile, research and development had mostly focused on organizational KM; therefore, this paper aims to review current personal KM adoption by construction project managers, which is an untapped area for current KM development.
Exact extraction of piezoresistance coefficient using flat membrane

The method for the extraction of piezoresistance coefficients with the use of a flat membrane as a test structure is considered. The necessary and sufficient conditions and conditioning of the extraction problem are examined as a problem of a correct test structure. For the given condition number, the number of the error propagation of the input data is considered.
Thyroid hormone induction of mitochondrial activity is coupled to mitophagy via ROS-AMPK-ULK1 signaling

Currently, there is limited understanding about hormonal regulation of mitochondrial turnover. Thyroid hormone (T3) increases oxidative phosphorylation (OXPHOS), which generates reactive oxygen species (ROS) that damage mitochondria. However, the mechanism for maintenance of mitochondrial activity and quality control by this hormone is not known. Here, we used both in vitro and in vivo hepatic cell models to demonstrate that induction of mitophagy by T3 is coupled to oxidative phosphorylation and ROS production. We show that T3 induction of ROS activates CAMKK2 (calcium/calmodulin-dependent protein kinase kinase 2, β) mediated phosphorylation of PRKAA1/AMPK (5′ AMP-activated protein kinase), which in turn phosphorylates ULK1 (unc-51 like autophagy activating kinase 1) leading to its mitochondrial recruitment and initiation of mitophagy. Furthermore, loss of ULK1 in T3-treated cells impairs both mitophagy as well as OXPHOS without affecting T3 induced general autophagy/lipophagy. These findings demonstrate a novel ROS-AMPK-ULK1 mechanism that couples T3-induced mitochondrial turnover with activity, wherein mitophagy is necessary not only for removing damaged mitochondria but also for sustaining efficient OXPHOS.
“Test Tube Cetaceans”: From the Evaluation of Susceptibility to the Study of Genotoxic Effects of Different Environmental Contaminants Using Cetacean Fibroblast Cell Cultures

© 2012 Marsili et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. “Test Tube Cetaceans”: From the Evaluation of Susceptibility to the Study of Genotoxic Effects of Different Environmental Contaminants Using Cetacean Fibroblast Cell Cultures
Quantitative EEG Signatures through Amplitude and Phase Modulation Patterns

Cortical spatiotemporal signal patterns based on object recognition can be discerned from visual stimulation. These are in the form of amplitude modulation (AM) and phase modulation (PM) patterns, which contain perceptual information gathered from sensory input. A high-density Electroencephalograph (EEG) device consisting of 48 electrodes with a spacing of 5 mm was utilized to measure frontal lobe activity in order to capture event-related potentials from visual stimuli. Four randomized stimuli representing different levels of salient responsiveness were measured to determine if mild stimuli can be discerned from more extreme stimuli. AM/PM response patterns were detected between mild and more salient stimuli across participants. AM patterns presented distinct signatures for each stimulus. AM patterns had the highest number of incidents detected in the middle of the frontal lobe. Through this work, we can expand our encyclopedia of neural signatures to object recognition, and provide a broader understanding of quantitative neural responses to external stimuli. The results provide a quantitative approach utilizing spatiotemporal patterns to analyze where distinct AM patterns can be linked to object perception.
Adaptive gray level run length features from class distance matrices

We constructed class distance matrices for the gray level run length texture analysis method. For a four-class problem of liver cell nuclei, we found that there exist areas of consistently high values in the class distance matrices. We combined the information from the entries of the normalized run length matrix, based on the class distance matrices, to obtain adaptive features for texture classification. Using this procedure, we extracted only two features, which halved the classification error when compared to the best pair of classical gray level run length matrix features.
Composition of feature space and state space dynamics models for model-based reinforcement learning (ニューロコンピューティング)

Learning a dynamics model and a reward model during reinforcement learning is a useful way, since the agent can also update its value function by using the models. In this paper, we propose a general dynamics model that is a composition of the feature space dynamics model and the state space dynamics model. This way enables to obtain a good generalization from a small number of samples because of the linearity of the state space dynamics, while it does not lose the accuracy. We demonstrate the simulation comparison of some dynamics models used together with a Dyna algorithm.
Diet and cancer of the prostate: a case‐control study in Greece

The nutritional aetiology of prostate cancer was evaluated in Athens, Greece, through a case‐control study that included 320 patients with histologically confirmed incident prostate cancer and 246 controls without history or symptomatology of benign prostatic hyperplasia or prostate cancer, treated in the same hospital as the cases for minor diseases or conditions. Among major food groups, milk and dairy products as well as added lipids were marginally positively associated with risk for prostate cancer. Among added lipids, seed oils were significantly and butter and margarine non‐significantly positively associated with prostate cancer risk, whereas olive oil was unrelated to this risk. Cooked tomatoes and to a lesser extent raw tomatoes were inversely associated with the risk for prostate cancer. In analyses focusing on nutrients, rather than foods, polyunsaturated fats were positively and vitamin E inversely associated with prostate cancer. We conclude that several nutrition‐related processes jointly contribute to prostate carcinogenesis. Int. J. Cancer 80:704–708, 1999. © 1999 Wiley‐Liss, Inc.
Three Transporters Mediate Uptake of Glycine Betaine and Carnitine by Listeria monocytogenes in Response to Hyperosmotic Stress

ABSTRACT The uptake and accumulation of the potent osmolytes glycine betaine and carnitine enable the food-borne pathogen Listeria monocytogenes to proliferate in environments of elevated osmotic stress, often rendering salt-based food preservation inadequate. To date, three osmolyte transport systems are known to operate in L. monocytogenes: glycine betaine porter I (BetL), glycine betaine porter II (Gbu), and a carnitine transporter OpuC. We investigated the specificity of each transporter towards each osmolyte by creating mutant derivatives of L. monocytogenes 10403S that possess each of the transporters in isolation. Kinetic and steady-state osmolyte accumulation data together with growth rate experiments demonstrated that osmotically activated glycine betaine transport is readily and effectively mediated by Gbu and BetL and to a lesser extent by OpuC. Osmotically stimulated carnitine transport was demonstrated for OpuC and Gbu regardless of the nature of stressing salt. BetL can mediate weak carnitine uptake in response to NaCl stress but not KCl stress. No other transporter in L. monocytogenes 10403S appears to be involved in osmotically stimulated transport of either osmolyte, since a triple mutant strain yielded neither transport nor accumulation of glycine betaine or carnitine and could not be rescued by either osmolyte when grown under elevated osmotic stress.
A Century of Ornithology in Nebraska: A Personal View

—The Nebraska Ornithologists’ Union cele‐ brated its centennial year during 1999. During more than 65 years it has published a quarterly journal, the Nebraska Bird Re‐ view, and has also published several proceedings of annual meetings as well as special or “occasional” publications. Dur‐ ing this same century one native Nebraska bird species (Pas‐ senger Pigeon) has become extinct, another (Eskimo Curlew) has possibly become extinct, and at least 15 species apparently have been extirpated as breeding species in the state. Addition‐ ally at least seven species have begun breeding successfully in the state, either through purposeful or accidental human ef‐ forts, or by range expansion and associated self‐introduction. Several species have also managed to re‐establish themselves after near extirpation or severe population decline. * Published in Contributions to the History of North American Ornithology, Volume II, edited by William E. Davis, Jr., and Jerome A. Jackson (Cambridge, MA: Nuttall Ornithological Club, 2000), pp. 347– 371. Copyright © 2000 Nuttall Ornithological Club. Used by permission. A Century of Ornithology in Nebraska 2 n attempt to summarize the history of a century of ornithology by a person who has witnessed only the last forty years of it, is perhaps as difficult as it is to describe an elephant when only its retreating rear end has been seen. Misinterpretation as well as an emphasis on the better‐known and closer portions are likely to occur. Furthermore, besides being a necessarily myopic view, the following account has a distinctly personal touch, inasmuch as I have seen Nebraska only through my own eyes and experiences. Yet, we have good documentation of the activities of ornithologists at the turn of the last century through the earliest publications of the Ne‐ braska Ornithologists’ Union, and these have helped to let me see the front of the elephant with some clarity. I hope others might agree. The history of scientific ornithology in the state began with the Lewis and Clark expedition, when the group passed northward through what is now Nebraska in July of 1804. About 25 species were observed by them at that time (Swenk 1935). Two decades later, a government expedition headed by Major S. H. Long passed through Nebraska in 1819–1820, and included the naturalist Thomas Say. They spent the winter near the present location of Council Bluffs, and observed a substan‐ tial number of species (Thwaites 1905). The Orange‐crowned Warbler (Vermivora celata) was discovered near Council Bluffs (perhaps on the Nebraska side) during this expedition. Still later, Prince Maximilian, together with his artist Karl Bodmer, passed upstream through Nebraska’s section of the Missouri in April and early May of 1833, and downstream again in May of 1834. At that time such species as the Whip‐poor‐will (Capri‐ mulgus vociferus) and Wood Duck (Aix sponsa) were heard or A
Attractor Neural Networks for Simulating Dyslexic Patients' Behavior

It was investigated that the ability of an attractor neural network. The attractor neural network can be applicable to various symptoms of brain damaged patients. It can account for delays in reaction times in word reading and word identification tasks. Because the iteration numbers of mutual connections between an output and a cleanup layers might increase, when they are partially damaged. This prolongation looks or behaves the delays of reaction times of brain damaged patients. When we applied the attractor neural network to the data of Tyler et al. (2000) for categorization task, it showed a kind of category specific phenomenon. In this sense, the attractor neural network could explain an aspect of the category specific disorders. In this sense the attractor network might simulate the human semantic memory organization. In spite of variations in data, and in spite of the simplicity of the architecture, the attractor network showed good performances. We could say that the attractor network succeeded in mimicking human normal subjects and brain damaged patients. The possibility of explaining the triangle model (Plaut & McClelland,1989; Plaut, McClelland, Seidenberg, and Patterson, 1996) also discussed.
Contribution of LCA approach to the choice of rotating electrical machines for environmental impact minimization

From usual point of view, electrical machine is designed and chosen in order to minimum initial investment for given characteristics. Eco-design is a new approach for motors design, it introduces additional environmental dimension to traditional choices method. It uses a Life Cycle Assessment (LCA) tools. This work highlights the LCA approach applied to AC machines. Then the global environmental costs of the machine are evaluated considering its total life cycle and according to normalised impact criteria. Finally, the implication of LCA approach to the choice of a standard electrical machine is realised in order to minimise the global environmental costs.
Study on converters for doubly fed induction generator based wind power generation system

Doubly-fed induction generator (DFIG) based wind power generation is connected to power grid via an electrical conversion system which consists of two back-to-back connected voltage source converters, i.e., rotor side converter (RSC) and grid side converter (GSC). Both converters have the same topology and working principles with different functions during operation. Hence, the characteristics and construct of three-phase voltage source PWM converters were first analyzed. Further, some auxiliary services with the converters were investigated such as voltage control capability, reactive power compensation capability, fault ride through capability and active harmonic filtering capability and so on, in respond to the stringent grid codes nowadays. An active harmonic filtering approach was presented. Simulation results illustrate good performance of the proposed system and control strategies.
New way to isolate simian virus 40 nucleoprotein complexes from infected cells: use of a thiol-specific reagent

A new method for the isolation of simian virus 40 nucleoprotein complexes from nuclei of lytically infected cells is described. The method is based on the addition of a thiol-specific reagent, 5'5'-dithiobis(2-nitrobenzoic acid), to lysis and extraction buffers. By inhibiting an uncoating activity during simian virus 40 extraction, 5'5'-dithiobis (2-nitrobenzoic acid) allows the use of efficient extraction buffers, such as one containing Triton X-100 and EDTA, for the isolation of native simian virus 40 minichromosomes and virion-type structures. Use of the method is illustrated by following encapsidation of simian virus 40 minichromosomes in a pulse-chase experiment. Since 5'5'-dithiobis (2-nitrobenzoic acid) is an inhibitor of many different enzymes, the 5',5'-dithiobis (2-nitrobenzoic acid) extraction technique may be useful for the isolation of not only papovaviruses but also other viruses and possibly cellular chromatin.
An iterative receiver for groupwise bit-interleaved coded QAM STBC OFDM

A groupwise bit-interleaved coded quadrature amplitude modulated (BICQAM) space-time block coded (STBC) orthogonal frequency division multiplexing (OFDM) system is studied in this paper, to exploit both the capacity and transmit diversity gains in wideband frequency selective channels. A "turbo" receiver is deployed to further exploit the diversity gains from receive antennas. Through iteratively exchanging soft information between the detector and the decoder, the receiver can achieve the performance of a single-group BICQAM STBC OFDM system after four to five iterations. Simplified interference estimation is then proposed to reduce the computational complexity. Simulation results show that only marginal performance degradation is introduced by this simplification.