Miracle-dz/UniFAR-FTUs huggingface dataset:
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface

The calculation of protein interaction energetics is of fundamental interest, yet accurate quantities are difficult to obtain due to the complex and dynamic nature of protein interfaces. This is further complicated by the presence of water molecules, which can exhibit transient interactions of variable duration and strength with the protein surface. The T-cell receptor (TCR) and its staphylococcal enterotoxin 3 (SEC3) binding partner are well-characterized examples of a protein−protein interaction system exhibiting interfacial plasticity, cooperativity, and additivity among mutants. Specifically engineered mutants induce intercalating interfacial water molecules, which subsequently enhance protein−protein binding affinity. In this work, we perform a set of molecular mechanics (MM) Poisson−Boltzmann (PB) surface area (SA) calculations on the wild type and two mutant TCR-SEC3 systems and show that the method is able to discriminate between weak and strong binders only when key explicit water molecules are included in the analysis. The results presented here point to the promise of MM-PBSA toward rationalizing molecular recognition at protein−protein interfaces, while establishing a general approach to handle explicit interfacial water molecules in such calculations.
Optimal Intervention Strategies for a SEIR Control Model of Ebola Epidemics

A SEIR control model describing the Ebola epidemic in a population of a constant size is considered over a given time interval. It contains two intervention control functions reflecting efforts to protect susceptible individuals from infected and exposed individuals. For this model, the problem of minimizing the weighted sum of total fractions of infected and exposed individuals and total costs of intervention control constraints at a given time interval is stated. For the analysis of the corresponding optimal controls, the Pontryagin maximum principle is used. According to it, these controls are bang-bang, and are determined using the same switching function. A linear non-autonomous system of differential equations, to which this function satisfies together with its corresponding auxiliary functions, is found. In order to estimate the number of zeroes of the switching function, the matrix of the linear non-autonomous system is transformed to an upper triangular form on the entire time interval and the generalized Rolle’s theorem is applied to the converted system of differential equations. It is found that the optimal controls of the original problem have at most two switchings. This fact allows the reduction of the original complex optimal control problem to the solution of a much simpler problem of conditional minimization of a function of two variables. Results of the numerical solution to this problem and their detailed analysis are provided.
A PT -Symmetric Dual-Core System with the Sine-Gordon Nonlinearity and Derivative Coupling

As an extension of the class of nonlinear PT -symmetric models, we propose a system of sine-Gordon equations, with the PT symmetry represented by balanced gain and loss in them. The equations are coupled by sine-field terms and first-order derivatives. The sinusoidal coupling stems from local interaction between adjacent particles in coupled Frenkel–Kontorova (FK) chains, while the cross-derivative coupling, which was not considered before, is induced by three-particle interactions, provided that the particles in the parallel FK chains move in different directions. Nonlinear modes are then studied in this system. In particular, kink-kink (KK) and kink-anti-kink (KA) complexes are explored by means of analytical and numerical methods. It is predicted analytically and confirmed numerically that the complexes are unstable for one sign of the sinusoidal coupling and stable for another. Stability regions are delineated in the underlying parameter space. Unstable complexes split into free kinks and anti-kinks that may propagate or become quiescent, depending on whether they are subject to gain or loss, respectively.
Cutaneous Leishmaniasis in North Africa: a review

In North African countries, cutaneous leishmaniasis transmission has been increasing since the 1980s, with a significant increase in the incidence of cases and a spread of the geographical distribution. The disease currently represents a major public health problem with a productivity gap and an impediment for development, which results in dramatic socioeconomic and psycho-sanitary impacts. The incidence is more than thousands of cases every year in Algeria, Libya, Morocco, and Tunisia. In Egypt, only a few dozen cases per year are reported, mainly in the Sinai Peninsula. Three Leishmania species, associated with distinct eco-epidemiological and clinical patterns, are involved, namely Leishmania infantum, L. major, and L. tropica. However, L. major is by far the most frequent in Algeria, Libya, and Tunisia, with more than 90% of the registered cases. It is mainly encountered in rural areas under semi-arid, arid and Saharan climates. Leishmania tropica is more prevalent in Morocco, reaching 30–40% of isolates in some districts. Much data is still missing concerning the risk factors of the infection and the lesion development, as well as vector and reservoir ecology and behavior. The knowledge of such parameters, following multidisciplinary and integrated approaches, is crucial for better management and control of the disease, that also faces a lack of resources and efficient control measures.
Energy-Efficient Routing Schemes for Underwater Acoustic Networks

Interest in underwater acoustic networks has grown rapidly with the desire to monitor the large portion of the world covered by oceans. Fundamental differences between underwater acoustic propagation and terrestrial radio propagation may call for new criteria for the design of networking protocols. In this paper, we focus on some of these fundamental differences, including attenuation and noise, propagation delays, and the dependence of usable bandwidth and transmit power on distance (which has not been extensively considered before in protocol design studies). Furthermore, the relationship between the energy consumptions of acoustic modems in various modes (i.e., transmit, receive, and idle) is different than that of their terrestrial radio counterparts, which also impacts the design of energy-efficient protocols. The main contribution of this work is an in-depth analysis of the impacts of these unique relationships. We present insights that are useful in guiding both protocol design and network deployment. We design a class of energy-efficient routing protocols for underwater sensor networks based on the insights gained in our analysis. These protocols are tested in a number of relevant network scenarios, and shown to significantly outperform other commonly used routing strategies and to provide near optimal total path energy consumption. Finally, we implement in ns2 a detailed model of the underwater acoustic channel, and study the performance of routing choices when used with a simple MAC protocol and a realistic PHY model, with special regard to such issues as interference and medium access.
Paper recommendation using citation proximity in bibliographic coupling

: Research paper recommendation has been a hot research area for the last few decades. Thus far, numerous diﬀerent paper recommendation approaches have been proposed. Some of these include methods based on metadata, content similarity, collaborative (cid:12)ltering, and citation analysis, among others. Citation analysis methods include bibliographic coupling and co-citation analysis. Much research has been done in the area of co-citation analysis. Researchers have also performed experiments using the proximity of in-text citations in co-citation analysis and have found that it improves the accuracy of paper recommendation. In co-citation analysis, the similarity is discovered based on the frequency of co-cited papers in diﬀerent research papers and those citing papers may belong to diﬀerent areas. However, when proximity is used to calculate co-citation, the accuracy of recommendations improves signi(cid:12)cantly. Bibliographic coupling (cid:12)nds bibliographic coupling strength based on the common references between two papers. In bibliographic coupling, a large number of common references of two papers means that they belong to the same area, unlike co-citation analysis, in which there is a possibility that the citing papers may belong to diﬀerent areas. Based on the observation that with the use of proximity analysis the accuracy in cases of co-citation analysis has improved, this paper investigates if the accuracy of paper recommendation can be further improved by using proximity analysis in bibliographic coupling. This paper proposes an approach that extends the traditional bibliographic coupling by exploiting the proximity of in-text citations of bibliographically coupled articles. The proposed approach takes into account the proximity of in-text citations by clustering the in-text citations using a density-based algorithm called DBSCAN. Experiments on a data set of research papers are presented to show that there is a substantial increase in accuracy of the recommendations produced by DBSCAN based on proximity analysis of in-text citations compared to traditional bibliographic coupling and content-based approaches.
Ball flight kinematics, release variability and in‐season performance in elite baseball pitching

The purpose of this study was to quantify ball flight kinematics (ball speed, spin rate, spin axis orientation, seam orientation) and release location variability in the four most common pitch types in baseball and relate them to in‐season pitching performance. Nine NCAA Division I pitchers threw four pitching variations (fastball, changeup, curveball, and slider) while a radar gun measured ball speed and a 600‐Hz video camera recorded the ball trajectory. Marks on the ball were digitized to measure ball flight kinematics and release location. Ball speed was highest in the fastball, though spin rate was similar in the fastball and breaking pitches. Two distinct spin axis orientations were noted: one characterizing the fastball and changeup, and another, the curveball and slider. The horizontal release location was significantly more variable than the vertical release location. In‐season pitching success was not correlated to any of the measured variables. These findings are instructive for inferring appropriate hand mechanics and spin types in each of the four pitches. Coaches should also be aware that ball flight kinematics might not directly relate to pitching success at the collegiate level. Therefore, talent identification and pitching evaluations should encompass other (e.g., cognitive, psychological, and physiological) factors.
PREDICTION OF SHRINKAGE STRESSES IN PAVEMENTS CONTAINING SOIL-CEMENT BASES

THE CREEP CHARACTERISTICS OF ALL OF THE MATERIALS IN THE PAVEMENT STRUCTURE TOGETHER WITH THE SHRINKAGE AND STRENGTH CHARACTERISTICS OF THE SOIL CEMENT ARE USED IN AN INCREMENTAL AXISYMMETRIC FINITE-ELEMENT SOLUTION TO THE PROBLEM OF SHRINKAGE CRACKING. STRESSES ARE PREDICTED AT SELECTED TIME INTERVALS BY INCREASING THE SHRINKAGE STRAINS IN THE SOIL CEMENT IN SMALL TIME INCREMENTS AND ALLOWING RELAXATION DUE TO CREEP TO OCCUR BEFORE SUPERPOSITION OF THE NEXT SHRINKAGE INCREMENT. TWO CASES ARE ANALYZED: ONE CONSIDERS A UNIFORM SHRINKAGE IN THE SOIL CEMENT; THE OTHER CONSIDERS A DIFFERENTIAL SHRINKAGE ASSUMING THAT DESICCATION BEGINS AT THE SURFACE OF THE SOIL-CEMENT BASE AND MIGRATES TOWARE THE INTERIOR. ALSO INCLUDED AS A BRIEF DISCUSSION OF THE INFLUENCE OF ASPHALT CONCRETE TEMPERATURE AND THERMAL EFFECTS ON THE MAGNITUDE OF THE SHRINKAGE STRESSES. /AUTHOR/
The Effect of Context on the EFL Learners' Idiom Processing Strategies.

The present study investigated the effect of context on the strategies the EFL learners utilized to process idioms. To do so, ten Iranian intermediate EFL learners were randomly assigned to two groups who then attended a think-aloud session. The 5 subjects in the first group were exposed to an animated cartoon including 23 unfamiliar idioms while their counterparts in the second group were exposed to the written version of the same material. The subjects of the two groups were asked to verbally report their thought processes when trying to define the unfamiliar idioms. The data thus gathered form the small sample revealed 8 major strategies which were then used to prepare a questionnaire to be administered to a larger sample. The new sample included 60 subjects randomly assigned to two groups of 30.The first group as in the think-aloud session was exposed to the animated cartoon while the other read the respective script. The subjects in both groups were asked to check the strategies they resorted to when guessing the meaning of unfamiliar idioms. The results of the study showed both inter and intra-group differences confirming the effect of context on the strategies applied in processing unfamiliar idioms.
Lipoperoxidation and Protein Oxidative Damage Exhibit Different Kinetics During Septic Shock

Septic shock (SS)-related multiorgan dysfunction has been associated with oxidative damage, but little is known about the temporal damage profile and its relationship to severity. The present work investigated prospectively 21 SS patients. Blood samples were obtained at diagnosis, 24, 72 hours, day 7, and at 3 months. At admission, thiobarbituric acid reactive substances (TBARSs), plasma protein carbonyls, plasma protein methionine sulfoxide (MS), ferric/reducing antioxidant power (FRAP), total red blood cell glutathione (RBCG), uric acid (UA), and bilirrubin levels were increased (P < .05). Total radical—trapping antioxidant potential (TRAP) and vitamin-E were similar to controls, and vitamin-C was decreased (P < .05). During evolution, TBARS and RBCG increased (P < .001), vitamin-E levels remained stable, whereas plasma protein carbonyls and MS, TRAP, vitamin-C, reduced glutathione, and UA levels decreased (P < .006). After 3 months, plasma protein carbonyls and MS persisted elevated. More severe patients exhibited higher TBARS, TRAP, FRAP, vitamin-C, UA, and bilirrubin levels. Our results suggest early and persistent oxidative stress during septic shock and a correlation between increasing levels of lipoperoxidation and sepsis severity.
Upregulation of cognitive control networks in older adults’ speech comprehension

Speech comprehension abilities decline with age and with age-related hearing loss, but it is unclear how this decline expresses in terms of central neural mechanisms. The current study examined neural speech processing in a group of older adults (aged 56–77, n = 16, with varying degrees of sensorineural hearing loss), and compared them to a cohort of young adults (aged 22–31, n = 30, self-reported normal hearing). In a functional MRI experiment, listeners heard and repeated back degraded sentences (4-band vocoded, where the temporal envelope of the acoustic signal is preserved, while the spectral information is substantially degraded). Behaviorally, older adults adapted to degraded speech at the same rate as young listeners, although their overall comprehension of degraded speech was lower. Neurally, both older and young adults relied on the left anterior insula for degraded more than clear speech perception. However, anterior insula engagement in older adults was dependent on hearing acuity. Young adults additionally employed the anterior cingulate cortex (ACC). Interestingly, this age group × degradation interaction was driven by a reduced dynamic range in older adults who displayed elevated levels of ACC activity for both degraded and clear speech, consistent with a persistent upregulation in cognitive control irrespective of task difficulty. For correct speech comprehension, older adults relied on the middle frontal gyrus in addition to a core speech comprehension network recruited by younger adults suggestive of a compensatory mechanism. Taken together, the results indicate that older adults increasingly recruit cognitive control networks, even under optimal listening conditions, at the expense of these systems’ dynamic range.
Independent responses to ultraviolet radiation and herbivore attack in broccoli

The plant responses to ultraviolet-B radiation (UV-B) and to insect herbivory are believed to be partially similar. In this study, responses to these factors were investigated in the crop species broccoli (Brassica oleracea L. convar. botrytis, Brassicaceae). Plants were first grown under three UV-B regimes (80%, 23%, and 4% transmittance of ambient UV-B) in greenhouses covered with either innovative materials (high and medium transmittance) or conventional glass (low transmittance). Half of the plants then remained under these conditions, but the other half were transferred to the field with ambient light and herbivore access for up to 3 d. The plant responses to distinct environmental conditions were examined by analysing the morphological and chemical parameters of plants kept inside and plants exposed in the field. Furthermore, suitability of field-exposed plants to naturally occurring insects was investigated in relation to UV-B pretreatment. High levels of UV-B radiation led to increased flavonoid concentrations, but to a lower biomass accumulation in broccoli. These patterns remained after outdoor exposure. However, UV-induced changes of plant traits did not alter attractiveness to herbivorous insects: thrips, whiteflies, and aphids attacked plants independently of UV-B pretreatment. A 3-fold increase of indolyl glucosinolate concentrations occurred in above-ground tissue of all the plants, most likely due to massive herbivore attack after 3 d of field exposure. The results show that plants respond with high specificity to different abiotic and biotic impacts, demonstrating the separate perception and processing of stress factors.
IL-8 reduces VCAM-1 secretion of smooth muscle cells by increasing p-ERK expression when 3-D co-cultured with vascular endothelial cells.

OBJECTIVE The goal of this study was to investigate the crosstalk between vascular endothelial cells (ECs) and smooth muscle cells (SMCs) using a three-dimensional (3-D) co-culture model. In addition, the role of IL-8 in this crosstalk was investigated. METHODS A 3-D co-culture model was constructed using a Transwell chamber system and type I collagen gel. Human umbilical artery smooth muscle cells (HUASMCs) were suspended in the gel and added to the upper compartment of the Transwell. Human umbilical vein endothelial cells (HUVECs) were then grown on the surface of the gel. The growth of HUASMCs was tested with a CFDA SE cell proliferation kit. IL-8 and other bioactive substances were investigated by ELISA and real-time PCR. The alteration of p-ERK expression related to the change in IL-8 levels was also examined by Western blot analysis. RESULTS The proliferation rate of HUASMCs in the 3-D co-culture model was 0.679 ± 0.057. Secretion and transcription of VEGF, t-PA, NO and VCAM-1 in the 3-D co-culture model were different than in single (2-D) culture. When 3-D co-cultured, IL-8 released by HUVECs was significantly increased (2.35 ± 0.16 fold) (P﹤0.05) and the expression of VCAM-1 from HUASMCs was reduced accordingly (0.55±0.09 fold). In addition, increasing or decreasing the level of IL-8 changed the level of p-ERK and VCAM-1 expression. The reduction of VCAM-1, resulting from increased IL-8, could be blocked by the MEK inhibitor, PD98059. CONCLUSION Crosstalk between HUVECs and HUASMCs occurred and was probably mediated by IL-8 in this 3-D co-culture model.
Hyperbaric oxygen for acute carbon monoxide poisoning.

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An Output-Sensitive Algorithm for Computing Visibility Graphs

The visibility graph of a set of nonintersecting polygonal obstacles in the plane is an undirected graph whose vertex set consists of the vertices of the obstacles and whose edges are pairs of vertices $(u,v)$ such that the open line segment between u and v does not intersect any of the obstacles. The visibility graph is an important combinatorial structure in computational geometry and is used in applications such as solving visibility problems and computing shortest paths. This paper presents an algorithm that computes the visibility graph of a set of obstacles in time $O(E + n\log n)$, where E is the number of edges in the visibility graph and n is the total number of vertices in all the obstacles.
Human hippocampal theta activity during virtual navigation

This study examines whether 4–8‐Hz theta oscillations can be seen in the human hippocampus, and whether these oscillations increase during virtual movement and searching, as they do in rodents. Recordings from both hippocampal and neocortical depth electrodes were analyzed while six epileptic patients played a virtual taxi‐driver game. During the game, the patients alternated between searching for passengers, whose locations were random, and delivering them to stores, whose locations remained constant. In both hippocampus and neocortex, theta increased during virtual movement in all phases of the game. Hippocampal and neocortical theta activity were also significantly correlated with each other, but this correlation did not differ between neocortex and hippocampus and within disparate neocortical electrodes. Our findings demonstrate the existence of movement‐related theta oscillations in human hippocampus, and suggest that both cortical and hippocampal oscillations play a role in attention and sensorimotor integration. © 2005 Wiley‐Liss, Inc.
Competencies in the 21 st century

Purpose – The purpose of this paper is to show that development of competencies needed to be effective managers and leaders requires program design and teaching methods focused on learning. This is the introductory essay to this special issue of JMD. Design/methodology/approach – Competencies are defined and an overview is provided for the eight papers that will follow with original research on competencies, their link to performance in various occupations, and their development. Findings – Emotional, social and cognitive intelligence competencies predict effectiveness in professional, management and leadership roles in many sectors of society. In addition, these competencies can be developed in adults. Research limitations/implications – As an introductory essay, this lays the foundation for the papers in this issue. Practical implications – Competencies needed to be effective can be developed. Originality/value – Despite widespread application, there are few published studies of the empirical link between competencies and performance. There are even fewer published studies showing that they can be developed. This special issue will add to both literatures.
Ultrafast magneto-optics in ferromagnetic III–V semiconductors

We investigate various ultrafast optical processes in ferromagnetic (III,Mn)V semiconductors induced by femtosecond laser pulses. Two-colour time-resolved magneto-optical spectroscopy has been developed, which allows us to observe a rich array of dynamical phenomena. We isolate several distinct temporal regimes in spin dynamics, interpreting the fast (<1 ps) dynamics as spin heating through sp–d exchange interaction between photo-carriers and Mn ions while the ∼100 ps component is interpreted as a manifestation of spin–lattice relaxation. Charge carrier and phonon dynamics were also carefully studied, showing an ultrashort charge lifetime of photo-injected electrons (∼2 ps) and propagating coherent acoustic phonon wavepackets with a strongly probe energy dependent oscillation period, amplitude and damping.