Miracle-dz/UniFAR-FTUs huggingface dataset:
ALADYN: a web server for aligning proteins by matching their large-scale motion

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. The latter often accompany functional conformational changes in proteins and enzymes. The ALADYN dynamics-based alignment can therefore highlight functionally-oriented correspondences that could be more elusive to sequence- or structure-based comparisons. The ALADYN server takes the structure files of the two proteins as input. The optimal relative positioning of the molecules is found by maximizing the similarity of the pattern of structural fluctuations which are calculated via an elastic network model. The resulting alignment is presented via an interactive graphical Java applet and is accompanied by a number of quantitative indicators and downloadable data files. The ALADYN web server is freely accessible at the http://aladyn.escience-lab.org address.
Identification of actin in situ at the ectoplasm-endoplasm interface of Nitella. Microfilament-chloroplast association

Using a glycerination procedure designed to avoid excessive plasmolysis or disruption of the ectoplasm, microfilaments in bundles at the ectoplasm-endoplasm interface of Nitella internode cell segments were found to bind rabbit heavy meromyosin (HMM) in situ. All HMM arrowheads in a bundle seem to have the same polarity and many lie in register as judged from the electron micrographs; the arrowhead periodicity is approximately 380 . The decorated microfilaments are thus similar to those seen in negatively stained cytoplasmic suspensions of internode cells. In glycerinated material, as well as in suspensions, the microfilaments are closely associated with chloroplasts. The microfilaments lie adjacent to or are attached to the chloroplast envelope. The results provide further evidence that the microfilaments thought to play a role in cytoplasmic streaming in vivo in Nitella consist of actin and suggest that they may be anchored to the chloroplasts.
The targets of vitamin D depend on the differentiation and activation status of CD4 positive T cells

Vitamin D is a potent immune system regulator. The active form of vitamin D (1,25(OH)2D3) suppresses the development of animal models of human autoimmune diseases. 1,25(OH)2D3 decreased the proliferation of all T helper (h) cells and decreased the production of IFN‐γ, IL‐2, and IL‐5. In Th2 cells 1,25(OH)2D3 increased the production of IL‐4. Quiescent CD4+ T cells express vitamin D receptors but only at a low level, which increased five‐fold following activation. 1,25(OH)2D3 treatment of Th0 cells, but not Th1 or Th2 cells, induced the expression of the transcription factor GATA‐3. Microarray technology identified over 102 targets of 1,25(OH)2D3 in CD4+ T cells. Of the 102 genes, 57 genes were down‐regulated and 45 were up‐regulated by 1,25(OH)2D3 treatment of the CD4+ T cells. Two of the identified genes are regulators of NFkB. Other genes of interest included the IL‐2Rβ gene and IgE binding factor. Th2 and Th0 cells produced more IgE binding factor after treatment with 1,25(OH)2D3 while Th1 cell IgE binding factor expression was unaffected by 1,25(OH)2D3 addition. It is unclear why some of the genes identified are expressed in CD4+ T cells and furthermore why 1,25(OH)2D3 regulates the expression of these genes. Clearly CD4+ T cells can be direct targets of vitamin D. The targets of vitamin D in CD4+ T cells depend on the state of activation and differentiation status of the cells. J. Cell. Biochem. 89: 922–932, 2003. © 2003 Wiley‐Liss, Inc.
Profiling of symmetric-encryption algorithms for a novel biomedical-implant architecture

Starting with the implantable pacemaker, microelectronic implants have been around for more than 50 years. A plethora of commercial and research-oriented devices have been developed so far for a wide range of biomedical applications. In view of an envisioned expanding implant market in the years to come, our ongoing research work is focusing on the specification and design of a novel biomedical microprocessor core, carefully tailored to a large subset of existing and future biomedical applications. Towards this end, we have taken steps in identifying various tasks commonly required by such applications and profiling their behavior and requirements. One such task is decryption of incoming commands to an implant and encryption of outgoing (telemetered) biological data. Secure bidirectional information relaying in implants has been largely overlooked so far although protection of personal (biological) data is very crucial. In this context, we evaluate a large number of symmetric (block) ciphers in terms of various metrics: average and peak power consumption, total energy budget, encryption rate and efficiency, program-code size and security level. For our study we use XTREM, a performance and power simulator for Intel's XScale embedded processor. Findings indicate the best-performing ciphers across most metrics to be MISTY1 (scores high in 5 out of 6 imposed metrics), IDEA and RC6 (both present in 4 out of 6 metrics). Further profiling of MISTY1 indicates a clear dominance of load/store, move and logic-operation instructions which gives us explicit directions for designing the architecture of our novel processor.
Acceleration of lung disease in children with cystic fibrosis after Pseudomonas aeruginosa acquisition

As part of the ongoing Wisconsin Cystic Fibrosis (CF) Neonatal Screening Project, we had the unique opportunity to study the longitudinal relationship between Pseudomonas aeruginosa (Pa) acquisition and infection and developing lung disease in children with CF. The primary objective was to determine whether acquisition of Pa was associated with a measurable change in the progression of lung disease. Two outcome measures were used to study 56 patients who were diagnosed through newborn screening: 1) Wisconsin additive chest radiograph score (WCXR), based on the average of scores from a pulmonologist and a radiologist, and 2) the highest forced expired volume in 1 sec (FEV1)/forced vital capacity (FVC) ratio. We used two measures of Pa acquisition: 1) time of first positive protocol‐determined oropharyngeal (with cough) culture, and 2) the magnitude of antibody titer detected by ELISA assays, using as antigen a crude cell lysate, purified exotoxin A, or an elastase toxoid prepared from three Pa strains. Other predictor variables included age, pancreatic status, height‐for age, and weight‐for‐age‐percentiles.
Effects of Transverse and Frontal Plane Knee Laxity on Hip and Knee Neuromechanics during Drop Landings

Background Varus-valgus (LAXVV) and internal-external (LAXIER) rotational knee laxity have received attention as potential contributing factors in anterior cruciate ligament injury. This study compared persons with above- and below-average LAXVV and LAXIER values on hip and knee neuromechanics during drop jump landings. Hypothesis People with greater LAXVV and LAXIER values will have greater challenges controlling frontal and transverse plane knee motions, as evidenced by greater joint excursions, joint moments, and muscle activation levels during the landing phase. Study Design Descriptive laboratory study. Methods Recreationally active participants (52 women and 44 men) between 18 and 30 years old were measured for LAXVV and LAXIER and for their muscle activation and transverse and frontal plane hip and knee kinetics and kinematics during the initial landing phase of a drop jump. The mean value was obtained for each sex, and those with above-average values on LAXVV and LAXIER (LAXHIGH = 17 women, 16 men) were compared with those with below-average values (LAXLOW = 18 women, 17 men). Results Women with LAXHIGH verus LAXLOW were initially positioned in greater hip adduction and knee valgus and also produced more prolonged internal hip adduction and knee varus moments as they moved toward greater hip adduction and internal rotation as the landing progressed. These patterns in LAX HIGH women were accompanied by greater prelanding and postlanding muscle activation amplitudes. Men with LAXHIGH versus LAXLOW also demonstrated greater hip adduction motion and produced greater internal hip internal rotation and knee varus and internal rotation moments. Conclusion Participants with greater LAXVV and LAXIER landed with greater hip and knee transverse and frontal plane hip and knee motions. Clinical Relevance People (especially, women) with increased frontal and transverse plane knee laxity demonstrate motions associated with noncontact anterior cruciate ligament injury mechanisms.
Phosphorus Fractionation Responds to Dynamic Redox Conditions in a Humid Tropical Forest Soil

Phosphorus (P) is a key limiting nutrient in highly weathered soils of humid tropical forests. A large proportion of P in these soils is bound to redox‐sensitive iron (Fe) minerals; however, little is known about how Fe redox interactions affect soil P cycling. In an incubation experiment, we changed bulk soil redox regimes by varying headspace conditions (air versus N2 gas) and examined the responses of soil P and Fe species to two fluctuating treatments (4‐ or 8‐day oxic followed by 4‐day anoxic) and two static redox treatments (oxic and anoxic). A static anoxic headspace increased NaOH‐extractable inorganic P and ammonium oxalate‐extractable total P (AO‐Pt) by 10% and 38%, respectively, relative to a static oxic headspace. Persistent anoxia also increased NaHCO3‐extractable total P (NaHCO3‐Pt) toward the end of the experiment. Effects of redox fluctuation were more complex and dependent on temporal scales. Ammonium oxalate‐extractable Fe and Pt concentrations responded to redox fluctuation early in the experiment, but not thereafter, suggesting a depletion of reductant over time. Immediately following a switch from an oxic to anoxic headspace, concentrations of AO‐Pt, AO‐Fe, and HCl‐extractable Fe(II) increased (within 30 min) but fell back to initial levels by 180 min. Surprisingly, the labile P pool (NaHCO3‐Pt) decreased immediately after reduction events, potentially due to resorption and microbial uptake. Overall, our data demonstrate that P fractions can respond rapidly to changes in soil redox conditions, and in environments where redox oscillation is common, roots and microbes may benefit from these rapid P dynamics.
Authors' Reply: association of HIV-infection and antiretroviral therapy with levels of endothelial progenitor cells and subclinical atherosclerosis.

REFERENCES 1. Gómez-Garre D, Estrada V, Ortega-Hernández A, et al. Association of HIV-infection and antiretroviral therapy with levels of endothelail progenitor cells and subclinical atherosclerosis. J Acquir Immune Defic Syndr. 2012;61:545551. 2. López M, Vispo E, San Román J, et al. High risk of endothelial dysfunction in HIV individuals may result from deregulation of circulating endothelial cells and endothelial progenitor cells. AIDS Res Hum Retroviruses. 2012;28:656–659. 3. Costiniuk CT, Hibbert BM, Filion LG, et al. Circulating endothelial progenitor cell levels are not reduced in HIV-infected men. J Infect Dis. 2012;205:713–717. 4. Papasavvas E, Hsue P, Reynolds G, et al. Increased CD34+/KDR+ cells are not associated with carotid artery intima-media thickness progression in chronic HIV-positive subjects. Antivir Ther. 2012;17:557–563. 5. Teofili L, Iachininoto MG, Capodimonti S, et al. Endothelial progenitor cell trafficking in human immunodeficiency virus-infected persons. AIDS. 2010;24:2443–2450. 6. López M, San Román J, Estrada V, et al. Cardiovascular disease risk in HIV infection and endothelial progenitor cells. J Infect Dis. 2012; 28:656–659. 7. Costiniuk CT, Hibbert BM, Filion LG, et al. Reply to: Cardiovascular disease risk in HIV infection and endothelial progenitor cells. J Infect Dis. 2012;205:713–717. 8. Asahara T, Murohara T, Sullivan A, et al. Isolation of putative progenitor endothelial cells for angiogenesis. Science. 1997;275:964–967. 9. Nuzzolo ER, Iachininoto MG, Teofili L. Endothelial progenitor cells and thrombosis. Thromb Res. 2012;129:309–313. 10. Mund JA, Case J. The ontogeny of endothelial progenitor cells through flow cytometry. Curr Opin Hematol. 2011;18:166–170. 11. Ingram DA, Mead LE, Tanaka H, et al. Identification of a novel hierarchy of endothelial progenitor cells using human peripheral and umbilical cord blood. Blood. 2004;104:2752–2760. 12. Yoder MC, Mead LE, Prater D, et al. Redefining endothelial progenitor cells via clonal analysis and hematopoietic stem/progenitor cell principals. Blood. 2007;109:1801–1809. 13. Mund JA, Estes ML, Yoder MC, et al. Flow cytometric identification and functional characterization of immature and mature circulating endothelial cells. Arterioscler Thromb Vasc Biol. 2012;32:1045–1053. 14. Pober JS. Just the FACS or stalking the elusive circulating endothelial progenitor cell. Arterioscler Thromb Vasc Biol. 2012;32:837–838.
Evaluating the effects of urbanization age on the morphology of low-order urban streams in the U.S. southern Piedmont

ABSTRACT We used space-for-time substitution, correlation, and regression analyses to study the effects of urbanization age on stream channel variables from 19 low-order urban watersheds in the southern Piedmont of the United States. The results are used to address questions regarding which variables are most responsive to urbanization age, the duration of response relative to system size, and changes in adjustment rate over time. Few morphological variables were found to be well correlated with metrics of urbanization age. The maximum-width/maximum-depth ratio (Wmax/Dmax) exhibited the best correlations to multiple metrics of urbanization age, with all correlations positive. A dearth of young urbanization ages in our dataset makes mathematically derived response times and end states for Wmax/Dmax highly uncertain. Inferences from the age range that is better represented suggest that the period of major response has occurred within the first three decades following urbanization. Subsequently, gradual increase in Wmax/Dmax appears to continue over 40 or more years. Response of channel form to urbanization and time elapsed in these low-order Piedmont streams is constrained by the presence of resistant bedrock below streambeds, a circumstance addressed by recent channel evolution models.
Feature-Based Choice and Similarity Perception in Normal-Form Games: An Experimental Study

In this paper, we claim that agents confronting with new interactive situations apply behavioral heuristics that drastically reduce the problem complexity either by neglecting the other players’ incentives, or by restricting attention to subsets of “salient” outcomes. We postulate that these heuristics are sensitive to the manipulation of those features that can be modified without altering the (Nash) equilibrium structure of the game. We call these features “descriptive”. We test experimentally the effect of these descriptive features on both choice behavior and cross-game similarity perception. Analysis of individual choices confirms our hypotheses, and suggests that non-equilibrium choices may derive from simplified mental models of the game structure, rather than from heterogeneous beliefs or limited iterative thinking. In addition, subjects tend to behave similarly in games sharing similar descriptive features, regardless of their strategic structure.
ALONGSHORE VARIABILITY OF COASTAL MORHODYNAMICS IN EASTERN LAKE ERIE DUE TO LOW FREQUENCY OSCILLATIONS OF LAKE LEVEL

Lake Erie has the fourth largest surface area, shallowest water depth and smallest volume among the five Great Lakes in North America (NOAA). The dominant wind direction over Lake Erieâ€™s is southwest-northeast, along the lakeâ€™s longitudinal axis. The atmospheric and water level data of the lake demonstrate that high wind and moving pressure systems can result in high storm surge of up to 3 m on the eastern end of the lake and significant drop in the water level at the western end of the lake Due to its shallow depth, such a water level gradient can trigger unique post-storm free water-level fluctuations or seiches in Lake Erie (Farhadzadeh, 2017). The morphodynamic implications of such low frequency oscillations are yet to be studied for the lakeâ€™s shorelines. Most of studies on the contributions of long waves to beach morphology changes focused on low frequency harmonics induced by short waves, e.g. infragravity waves, edge waves, etc., oscillations with periods of up to a few minutes. Wright and Short (1984) discussed the differences in hydrodynamic processes and relative contributions of various mechanisms to morphological changes of beaches of different states, i.e., reflective, dissipative or intermediate. They concluded that for reflective beaches, incident waves and subharmonic edge waves are dominant while for dissipative beaches currents associated with infragravity standing waves are dominant in nearshore areas. Russell (1993) stated that as low frequency wave energy increases toward a shoreline, the offshore-directed transport at low frequency can become more pronounced.
A review of available pesticide leaching models: Selection of models for simulation of herbicide fate in Finnish sugar beet cultivation

The quality of simulation results depends on the model structure and its parameterisation. The aim of this study was to find the best available models for herbicide fate simulation for Finnish conditions. Subjective model selection criteria were developed for the simulation domain: pesticide fate in Finnish sugar beet cultivation. An inventory was made of available models and a number of different pesticide and solute transport models were identified. Thirteen one-dimensional deterministic models (CRACK-NP, EPIC, GLEAMS, LEACHP, MACRO, OPUS, PELMO, PEARL, PESTLA, PLM, PRZM, RZWQM and SIMULAT) were compared and evaluated for their characteristics. The comparison showed that none of these models fulfilled all of the desired criteria. Finally, MACRO 4.1 and GLEAMS 3.0 were selected for herbicide fate simulations. The other high regarded models were RZWQM, PEARL and PELMO.
An analysis of the Burrows-Wheeler transform

The Burrows—Wheeler Transform (also known as Block-Sorting) is at the base of compression algorithms that are the state of the art in lossless data compression. In this paper, we analyze two algorithms that use this technique. The first one is the original algorithm described by Burrows and Wheeler, which, despite its simplicity outperforms the Gzip compressor. The second one uses an additional run-length encoding step to improve compression. We prove that the compression ratio of both algorithms can be bounded in terms of the kth order empirical entropy of the input string for any k ≥ 0. We make no assumptions on the input and we obtain bounds which hold in the worst case that is for every possible input string. All previous results for Block-Sorting algorithms were concerned with the average compression ratio and have been established assuming that the input comes from a finite-order Markov source.
Physical Factors Influencing Pleasant Touch during Passive Fingertip Stimulation

Objective Tactile explorations with the fingertips provide information regarding the physical properties of surfaces and their relative pleasantness. Previously, we performed an investigation in the active touch domain and linked several surface properties (i.e. frictional force fluctuations and net friction) with their pleasantness levels. The aim of the present study was to investigate physical factors being important for pleasantness perception during passive fingertip stimulation. Specifically we were interested to see whether factors, such as surfaces' topographies or their frictional characteristics could influence pleasantness. Furthermore, we ascertained how the stimulus pleasantness level was impacted by (i) the normal force of stimulus application (FN) and (ii) the stimulus temperature (TS). Methods and Results The right index fingertips of 22 blindfolded participants were stimulated using 27 different stimuli, which varied in average roughness (Ra) and TS. A 4-axis robot moved the stimuli horizontally under participants' fingertips with three levels of FN. The robot was equipped with force sensors, which recorded the FN and friction force (FT) during stimulation. Participants rated each stimulus according to a three-level pleasantness scale, as very pleasant (scored 0), pleasant (scored 1), or unpleasant (scored 2). These ordinal pleasantness ratings were logarithmically transformed into linear and unidimensional pleasantness measures with the Rasch model. Statistical analyses were conducted to investigate a possible link between the stimulus properties (i.e. Ra, FN, FT, and TS) and their respective pleasantness levels. Only the mean Ra and FT values were negatively correlated with pleasantness. No significant correlation was detected between FN or TS and pleasantness. Conclusion Pleasantness perception, resulting from passive fingertip stimulation, seems to be influenced by the surfaces' average roughness levels and average FT occurring during fingertip stimulation.
Local error estimates for discontinuous solutions of nonlinear hyperbolic equations

Let $u(x,t)$ be the possibly discontinuous entropy solution of a nonlinear scalar conservation law with smooth initial data. Suppose $u_\varepsilon (x,t)$ is the solution of an approximate viscosity regularization, where $\varepsilon > 0$ is the small viscosity amplitude. It is shown that by post-processing the small viscosity approximation $u_\varepsilon $, pointwise values of u and its derivatives with an error as close to e as desired can be recovered.The analysis relies on the adjoint problem of the forward error equation, which in this case amounts to a backward linear transport equation with discontinuous coefficients. The novelty of our approach is to use a (generalized) E-condition of the forward problem in order to deduce a $W^{1,\infty } $-energy estimate for the discontinuous backward transport equation; this, in turn, leads to e-uniform estimate on moments of the error $u_\varepsilon - u$. The approach presented does not “follow the characteristics” and, therefore, applies mutatis mutandis to o.
Unilateral Renal Cystic Disease: CT Findings

Unilateral renal cystic disease (URCD) is characterized by replacement of most of one kidney by multiple cysts scattered diffusely throughout the parenchyma without the formation of a distinct, encapsulated renal mass. There are no cysts in the opposite kidney or liver. The condition is nonfamilial and does not cause renal functional impairment. We describe the clinical and radiologic findings in two patients with URCD and discuss how the disorder usually can be distinguished from other renal cystic diseases using CT. Absence of a family history of renal cystic disease and the normality of the other kidney help distinguish URCD from autosomal dominant polycystic kidney disease. The diffuse nature of the cysts in URCD and the absence of a distinct encapsulated renal mass help distinguish URCD from cystic renal neoplasms.
Role of capecitabine in treating metastatic colorectal cancer in Chinese patients

The China Food and Drug Administration approved the use of capecitabine in patients with metastatic colorectal cancer (mCRC) in 2004. This paper reviews the available information of capecitabine in Chinese patients with mCRC, focusing on its effectiveness and safety against mCRC. Identification of all eligible studies was made by searching the PubMed and Wanfang database from 2000 to 2013. Published data examining various aspects of clinical response and tolerability with capecitabine alone or in combination with other chemotherapeutic or biological agents for first- and second-line mCRC were examined. Capecitabine and its combination displayed high efficacy in Chinese patients with mCRC. Toxicities are generally manageable, and elderly patients can tolerate capecitabine well.