Miracle-dz/UniFAR-FTUs huggingface dataset:
Light Chain– dependent Regulation of Kinesin's Interaction with Microtubules

We have investigated the mechanism by which conventional kinesin is prevented from binding to microtubules (MTs) when not transporting cargo. Kinesin heavy chain (HC) was expressed in COS cells either alone or with kinesin light chain (LC). Immunofluorescence microscopy and MT cosedimentation experiments demonstrate that the binding of HC to MTs is inhibited by coexpression of LC. Association between the chains involves the LC NH2-terminal domain, including the heptad repeats, and requires a region of HC that includes the conserved region of the stalk domain and the NH2 terminus of the tail domain. Inhibition of MT binding requires in addition the COOH-terminal 64 amino acids of HC. Interaction between the tail and the motor domains of HC is supported by sedimentation experiments that indicate that kinesin is in a folded conformation. A pH shift from 7.2 to 6.8 releases inhibition of kinesin without changing its sedimentation behavior. Endogenous kinesin in COS cells also shows pH-sensitive inhibition of MT binding. Taken together, our results provide evidence that a function of LC is to keep kinesin in an inactive ground state by inducing an interaction between the tail and motor domains of HC; activation for cargo transport may be triggered by a small conformational change that releases the inhibition of the motor domain for MT binding.
Phylogeny, niche conservatism and the latitudinal diversity gradient in mammals

Biologists have long searched for mechanisms responsible for the increase in species richness with decreasing latitude. The strong correlation between species richness and climate is frequently interpreted as reflecting a causal link via processes linked to energy or evolutionary rates. Here, we investigate how the aggregation of clades, as dictated by phylogeny, can give rise to significant climate–richness gradients without gradients in diversification or environmental carrying capacity. The relationship between climate and species richness varies considerably between clades, regions and time periods in a global-scale phylogenetically informed analysis of all terrestrial mammal species. Many young clades show negative richness–temperature slopes (more species at cooler temperatures), with the ages of these clades coinciding with the expansion of temperate climate zones in the late Eocene. In carnivores, we find steeply positive richness–temperature slopes in clades with restricted distributions and tropical origins (e.g. cat clade), whereas widespread, temperate clades exhibit shallow, negative slopes (e.g. dog–bear clade). We show that the slope of the global climate–richness gradient in mammals is driven by aggregating Chiroptera (bats) with their Eutherian sister group. Our findings indicate that the evolutionary history should be accounted for as part of any search for causal links between environment and species richness.
Establishment and Characterization of an Air-Liquid Canine Corneal Organ Culture Model To Study Acute Herpes Keratitis

ABSTRACT Despite the clinical importance of herpes simplex virus (HSV)-induced ocular disease, the underlying pathophysiology of the disease remains poorly understood, in part due to the lack of adequate virus–natural-host models in which to study the cellular and viral factors involved in acute corneal infection. We developed an air-liquid canine corneal organ culture model and evaluated its susceptibility to canine herpesvirus type 1 (CHV-1) in order to study ocular herpes in a physiologically relevant natural host model. Canine corneas were maintained in culture at an air-liquid interface for up to 25 days, and no degenerative changes were observed in the corneal epithelium during cultivation using histology for morphometric analyses, terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assays, and transmission electron microscopy (TEM). Next, canine corneas were inoculated with CHV-1 for 48 h, and at that time point postinfection, viral plaques could be visualized in the corneal epithelium and viral DNA copies were detected in both the infected corneas and culture supernatants. In addition, we found that canine corneas produced proinflammatory cytokines in response to CHV-1 infection similarly to what has been described for HSV-1. This emphasizes the value of our model as a virus–natural-host model to study ocular herpesvirus infections. IMPORTANCE This study is the first to describe the establishment of an air-liquid canine corneal organ culture model as a useful model to study ocular herpesvirus infections. The advantages of this physiologically relevant model include the fact that (i) it provides a system in which ocular herpes can be studied in a virus–natural-host setting and (ii) it reduces the number of experimental animals needed. In addition, this long-term explant culture model may also facilitate research in other fields where noninfectious and infectious ocular diseases of dogs and humans are being studied.
Development of pileup recovery algorithms by peak detection method of digital gamma ray spectroscopy

The Pulse pile-up in gamma ray spectroscopy is a severe problem because it degrades both energy resolution and detection efficiency, especially at high count rates. This paper presents two algorithms for signal recovery of peak pile up. These algorithms depend on experimental acquisition of gamma radiation signals with analog to digital converter at sampling rate 16MS/s. The first algorithm depends on a peak detection method that determines the peaks' parameters, which are recorded into a two rows matrix representing the amplitude and position of the peaks. The second algorithm depends on a peak sensitivity method, which determines the location of the maximum peaks using a local extreme method. The variance between each two adjacent points are calculated to find indices of nonzero elements that are larger than zero to determine the maximum amplitude of each peak. The resultant peaks correspond to peak location. These two methods are evaluated by comparing not only their parameters but also their fitting error. Moreover, the influence of these algorithms on the obtained spectrums are analyzed and evaluated. The results show that the second algorithm outperforms the performance of the first one due to the efficient recovery of overlapping peaks.
Use of fuzzy-logic-inspired features to improve bacterial recognition through classifier fusion

Escherichia coli O157:H7 has been found to cause serious health problems. Traditional methods to identify the organism are quite slow, pulsed-held gel electrophoresis (PFGE) images contain "banding pattern" information which can be used to recognize the bacteria. A fuzzy logic rule-based system is used as a guide to find a good feature set for the recognition of E. coli O157:H7. While the fuzzy rule-based system achieved good recognition, the human inspired features used in the rules were incorporated into a multiple neural network fusion approach which gave excellent separation of the target bacteria. The fuzzy integral was utilized in the fusion of neural networks trained with different feature sets to reach an almost perfect classification rate of E. coli O157:H7 PFGE patterns made available for the experiments.
A Rare Cause of Pulmonary Embolism and Seizure in a Young Man: Antiphospholipid Syndrome.

UNLABELLED Pulmonary embolism (PE) is a complication of underlying vascular thrombosis. The causes of PE are multi-factorial, and patients with PE present with various symptoms. We herein have presented the case of a 21-year-old man who initially developed palpitation, dyspnea, and seizure. Computed tomography of the chest ultimately indicated PE, and antiphospholipid syndrome (APS) was diagnosed with clinical thrombosis events and series presence of antiphospholipid antibodies. APS commonly causes vascular thrombosis within the vascular tree; however, nonthrombotic manifestations, such as seizure, may also occur. Clinicians should be aware of such non-thrombotic manifestations of APS to avoid misdiagnosis and inappropriate management. KEY WORDS Antiphospholipid syndrome • Pulmonary embolism • Seizure.
Mechanisms and therapeutic challenges in autism spectrum disorders: insights from Rett syndrome.

PURPOSE OF REVIEW A major challenge for understanding neurodevelopmental disorders, including autism spectrum disorders (ASDs), is to advance the findings from gene discovery to an exposition of neurobiological mechanisms that underlie these disorders and subsequently translate this knowledge into mechanism-based therapeutics. A promising way to proceed is revealed by the recent studies of rare subsets of ASDs. In this review, we summarize the latest advances in the mechanisms and emerging therapeutics for a rare single-gene ASD, Rett syndrome. RECENT FINDINGS Rett syndrome is caused by mutations in the gene coding for methyl CpG-binding protein 2 (MeCP2). Although MeCP2 has diverse functions, examination of MeCP2 mutant mice suggests the hypothesis that MeCP2 deficiency leads to aberrant maturation and maintenance of synapses and circuits in multiple brain systems. Some of the deficits arise from alterations in specific intracellular pathways such as the PI3K/Akt signaling pathway. These abnormalities can be at least partially rescued in MeCP2 mutant mice by treatment with therapeutic agents. SUMMARY Mechanism-based therapeutics are emerging for single-gene neurodevelopmental disorders such as Rett syndrome. Given the complexity of MeCP2 function, future directions include combination therapeutics that target multiple molecules and pathways. Such approaches will likely be applicable to other ASDs as well.
A relational approach to software metrics

There is still no standardization of software measures and metrics extraction tools have to be updated frequently to handle the changes. A possible solution is represented by using an intermediate abstraction layer to decouple the information extraction process from the use of the information. In this way a metrics researcher do not have to deal with language parsing production concepts such as declarations, class specifiers, and base clauses. This paper presents WebMetrics, an automated tool for software metrics collection. The tool uses, as intermediate layer, a set of intuitive relations to describe the source code structure. These relations are stored in a database in order to calculate metrics directly by performing SQL queries. To test the architecture, we applied the tool to the source code of an opensource project in order to compute CK metrics suite.
Irritability and Emotion Perception in Young Adults

Severe irritability is impairing to affected individuals and those around them. Literature on irritability and social functioning is growing with a focus on face emotion identification tasks. Most studies, however, have been conducted in children and adolescents, leaving a gap in the literature on adults. This study sought to determine how state irritability, induced during a frustrating computer task, and trait irritability, measured through self-report questionnaires, related to the performance of seventy-five undergraduate students on a face emotion morphing task. Responses to anger were of particular interest and explored through a hostile attribution bias. During the task participants viewed brief movies of faces morphing from a neutral to a 100% prototypical emotional facial expression and were asked to stop the movie when they detected the face emotion. Participants in the frustration condition and participants with high trait irritability were expected to require greater emotional intensity in a facial expression in order to identify non-angry emotions and less intensity in order to identify anger. Results indicated that, although the frustration manipulation was successful, participants in the frustration and nonfrustration conditions identified emotions at equal intensities. Participants in the frustration condition also identified happiness – the most easily identifiable emotion, and anger at comparable intensities. Trait irritability was unrelated to overall emotion intensity but correlated with hostile attribution biases. These findings suggest that the study of irritability and emotion identification should distinguish between state and trait irritability.
La gestión de marketing de ciudades y áreas metropolitanas: de la orientación al producto a la orientación al marketing

The application of marketing principles in the administration of cities has been usually reduced to the use of the communication tools to try to diffuse the city’s image among the different target publics. At the same time, the development of cities has habitually been based on the endowment of infrastructures and singular buildings, by means of relatively opaque strategic planning processes. From a marketing vision, we consider indispensable to base the development of cities on the active citizenship participation, as well as in the empowerment of the tangible and intangible aspects. In the case of the Metropolitan Bilbao, the strategic plan that has been developed in the last decade was centered on tangible elements, while the new plan puts a special emphasis on the intangible aspects and civic participation.
Cleavage of Arabidopsis PBS1 by a Bacterial Type III Effector

Plant disease-resistance (R) proteins are thought to function as receptors for ligands produced directly or indirectly by pathogen avirulence (Avr) proteins. The biochemical functions of most Avr proteins are unknown, and the mechanisms by which they activate R proteins have not been determined. In Arabidopsis, resistance to Pseudomonas syringae strains expressing AvrPphB requires RPS5, a member of the class of R proteins that have a predicted nucleotide-binding site and leucine-rich repeats, and PBS1, a protein kinase. AvrPphB was found to proteolytically cleave PBS1, and this cleavage was required for RPS5-mediated resistance, which indicates that AvrPphB is detected indirectly via its enzymatic activity.
MOLECULAR, CELLULAR AND DEVELOPMENTAL BIOLOGY

The undergraduate program in molecular, cellular and developmental biology (MCDB) is directed toward understanding the molecular and cellular mechanisms that provide the basis for biological structure, growth, evolution, embryonic development and genetic inheritance. Undergraduate majors learn about the scientific method, experimental approaches and groundbreaking discoveries that have made modern molecular and cellular biology such an important force in medicine, agriculture, and the growing biotechnology industry. They also learn about the diverse tools of modern biology, including recombinant DNA, genomic mapping, transgenic organisms, gene targeting, analysis of mutants, biochemical purification, antibody probes, laser manipulation of living cells, light and electron microscopy, and computer modeling. In addition to academic and laboratory classes, MCDB majors have many opportunities to participate in ongoing research in the department.
Effect of the INSIGHT Responsive Parenting Intervention on Rapid Infant Weight Gain and Overweight Status at Age 1 Year: A Randomized Clinical Trial.

IMPORTANCE Rapid infant weight gain is associated with later obesity, but interventions to prevent rapid infant growth and reduce risk for overweight status in infancy are lacking. OBJECTIVE To examine the effect of a responsive parenting (RP) intervention on infant weight gain between birth and 28 weeks and overweight status at age 1 year. DESIGN, SETTING, AND PARTICIPANTS The Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) study is an ongoing randomized clinical trial comparing an RP intervention designed to prevent childhood obesity with a safety control. The study includes primiparous mother-newborn dyads (n = 291) and was conducted at the Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, in addition to home visits. Enrollment was initiated in January 2012, and evaluable population analyses for this study were conducted between April 2015 and November 2015. INTERVENTIONS At 2 weeks post partum, initial intervention materials appropriate to the assigned treatment group were mailed to the participant's home. Research nurses conducted home visits at 3 weeks, 16 weeks, 28 weeks, and 40 weeks, and a research center visit occurred at 1 year. The Intervention Nurses Start Infants Growing on Healthy Trajectories curriculum included messages about infant feeding, sleep hygiene, active social play, emotion regulation, and growth record education. The control group received a developmentally appropriate home safety intervention also delivered by nurse home visitors. MAIN OUTCOMES AND MEASURES Conditional weight gain from birth to 28 weeks was calculated. General linear models examined intervention effect on conditional weight gain. The intervention's effect on infant weight-for-length percentiles was tested using analysis of variance. Logistic regression compared the odds of overweight status (weight for length ≥95th percentile) at 1 year as a function of conditional weight gain. RESULTS Of the mothers included in the study, 246 were white (88%), 260 were non-Hispanic (93%), 210 were married (75%), and 201 were working full time (72%) at time of enrollment. The mean conditional weight gain score was lower among infants in the RP group compared with the control group (-0.18; 95% CI, -0.36 to -0.001), reflecting that the RP infants gained weight more slowly than control group infants (0.18; 95% CI, 0.02-0.34); this effect did not differ by feeding mode (predominantly fed breast milk or not). Infants in the RP group also had lower mean weight-for-length percentiles at 1 year than infants in the control group (57.5%; 95% CI, 52.56%-62.37% vs 64.4%; 95% CI, 59.94%-69.26%; P = .04) and were less likely to be overweight at age 1 year (5.5% vs 12.7%; P = .05). CONCLUSIONS AND RELEVANCE An RP intervention is associated with reduced rapid weight gain during the first 6 months after birth and overweight status at age 1 year. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01167270.
Input Elaboration, Head Faithfulness and Evidence for Representation in the Acquisition of Left-edge Clusters in West Germanic

Several recent investigations of the development of left-edge clusters in West Germanic languages have demonstrated that the relative sonority of adjacent consonants plays a key role in children’s reduction patterns (e.g. Fikkert 1994, Gilbers & Den Ouden 1994, Chin 1996, Barlow 1997, Bernhardt & Stemberger 1998, Gierut 1999, Ohala 1999, Gnanadesikan this volume). These authors have argued that, for a number of children, at the stage in development when only one member of a left-edge cluster is produced, it is the least sonorous segment that survives, regardless of where this segment appears in the target string or the structural position that it occupies (head, dependent, or appendix). To briefly illustrate, while the more sonorous /S/ 2 is lost in favour of the stop in /S/+stop clusters, /S/ is retained in /S/+sonorant clusters; similarly, the least sonorous stop survives in both /S/+stop and stop+sonorant clusters, in spite of the fact that it occurs in different positions in the two strings. To account for reduction patterns such as these, a structural difference between /S/-initial and stop-initial clusters need not be assumed. This would seem to fare well in view of much of the recent constraint-based literature which de-emphasises the role of prosodic constituency in favour of phonetically-based explanations of phonological phenomena (see e.g. Hamilton 1996, Wright 1996, Kochetov 1999, Steriade 1999, Cote 2000). In this paper, we focus on a second set of reduction patterns for left-edge clusters, one which is not addressed in most of the sonority-based literature on cluster reduction in child language (L1): these patterns reveal a preference for structural heads to survive. For example, while the stop is retained in clusters of the shape /S/+stop and stop+sonorant, it is the sonorant that survives in /S/+sonorant clusters. The only sources that we have found where explicit reference is made to the retention of heads are Spencer (1986), who reanalyses Amahl’s data
Detection and Evaluation of Taylor Cones and Stable Jets on Wire Electrospinning Process

Here we come up with the novel idea of production quality management that will be based on the correlation of data on-line system with inputs of materials and spinning conditions and output information of nano fibrous layer. This paper demonstrates application of optical monitoring on NanospiderTM, technology and has wider impact on understanding the process on wire with moving carriage than fiber diameter relation only, unlike the stationary needle process. It concerns to statistical behavior of the process with other unknown parameters, like number droplets and spinning jets per unit length of wire, direction of jets, droplet size and geometry, droplet lifetime, stability and way of consumption, wire vibrations etc. We also designed the illuminating system according to further image analysis presented as signal in data series. Here we have come out from this empirical knowledge and we used computer visualization for process analyzing. The basic idea was the detection of the stable parts and the raising jets of fibers.
A preliminary study of the effect of ammonia on particle nucleation in the marine boundary layer

A ternary nucleation model for the H2SO4-NH3-H2O system is presented in an effort to examine the effect of NH3 on heteromolecular homogeneous nucleation in the marine boundary layer (MBL). The results from this nucleation model suggest that ammonia could, in fact, enhance the nucleation rate over that of the binary system, H2SO4-H2O. The magnitude of this enhancement is introduced as an enhancement ratio, which, in principle, is applicable to any binary nucleation rate for H2SO4-H2O. Also presented are preliminary results from a simple aerosol model using this enhancement ratio. These results suggest that under conditions typical of the marine environment it may be possible to produce enough particles to balance the various particle sinks characteristic of the MBL.
A qualitative comparison of three aspect mining techniques

The fact that crosscutting concerns (aspects) cannot be well modularized in object oriented software is an impediment to program comprehension: the implementation of a concern is typically scattered over many locations and tangled with the implementation of other concerns, resulting in a system that is hard to explore and understand. Aspect mining aims to identify crosscutting concerns in a system, thereby improving the system's comprehensibility and enabling migration of existing (object-oriented) programs to aspect-oriented ones. In this paper, we compare three aspect mining techniques that were developed independently by different research teams: fan-in analysis, identifier analysis and dynamic analysis. We apply each technique to the same case (JHotDraw) and mutually compare the individual results of each technique based on the discovered aspects and on the level of detail and quality of those aspects. Strengths, weaknesses and underlying assumptions of each technique are discussed, as well as their complementarity. We conclude with a discussion of possible ways to combine the techniques in order to achieve a better overall aspect-mining technique.
Vitamin K series: current status and future prospects

Abstract The Vitamin K series, particularly menaquinone, have been attracting research attention, due to the potential in reducing both osteoporosis and cardiovascular diseases. This review provides an overview of the types of vitamin K and their health benefits. This is followed by a critical review of the various biotechnological approaches used in the production of menaquinone, including solid and liquid state fermentations, extraction and recovery. The currently available market information is summarized and future growth prospects are discussed. Recommendations are also given for areas of future research in order to improve the production process for menaquinone and reduce costs.