Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying Rates of Evolutionary Adaptation in Response to Ocean Acidification

The global acidification of the earth's oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified. Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO2 conditions compared to the mussel species Mytilus trossulus. Using these measures we demonstrate that S. franciscanus may have faster evolutionary responses within 50 years of the onset of predicted year-2100 CO2 conditions despite having lower population turnover rates. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species.
Coreference between subjective expression and holder: A classification perspective

Instead of applying the traditional keyword spotting approach, the presence of coreference between the holders and their subjective expressions often becomes important to identify and classify opinion and sentiment, accurately. In the present task, we have developed a classification system to resolve coreference of subjective expressions with their holders and thus automate the process of text annotations. The dependency parsed features in addition to sentiment words helped in classifying the corefered instances using machine learning framework.
Optimization of micropatterned poly(lactic-co-glycolic acid) films for enhancing dorsal root ganglion cell orientation and extension

Nerve conduits have been a viable alternative to the ‘gold standard’ autograft for treating small peripheral nerve gap injuries. However, they often produce inadequate functional recovery outcomes and are ineffective in large gap injuries. Ridge/groove surface micropatterning has been shown to promote neural cell orientation and guide growth. However, optimization of the ratio of ridge/groove parameters to promote orientation and extension for dorsal root ganglion (DRG) cells on poly(lactic-co-glycolic acid) (PLGA) films has not been previously conducted. Photolithography and micro-molding were used to define various combinations of ridge/groove dimensions on PLGA films. The DRG cells obtained from chicken embryos were cultured on micropatterned PLGA films for cell orientation and migration evaluation. Biodegradation of the films occurred during the test period, however, this did not cause deformation or distortion of the micropatterns. Results from the DRG cell orientation test suggest that when the ridge/groove ratio equals 1 (ridge/groove width parameters are equal, i.e., 10 μm/10 μm (even)), the degree of alignment depends on the size of the ridges and grooves, when the ratio is smaller than 1 (groove controlled) the alignment increases as the ridge size decreases, and when the ratio is larger than 1 (ridge controlled), the alignment is reduced as the width of the grooves decreases. The migration rate and neurite extension of DRG neurons were greatest on 10 μm/10 μm and 30 μm/30 μm micropatterned PLGA films. Based on the data, the 10 μm/10 μm and 30 μm/30 μm micropatterned PLGA films are the optimized ridge/groove surface patterns for the construction of nerve repair devices.
GloSE-Lab: Teaching Global Software Engineering

In practice, more and more software development projects are distributed, ranging from partly distributed teams to global projects with each stakeholder located differently. Teaching actual practice in software engineering at university needs a proper mixture of theory and practice. But setting up practical exercises for global software engineering is hard, because students have to cooperate across different locations and situations reflecting the teaching intentions have to be provoked explicitly. This paper presents the concepts behind our common teaching environment for global software engineering - the GloSELab. It describes the experiences on setting up a distributed course and reports our teaching intentions based on each universities main focus: project management, requirements engineering & quality assurance, architecture, and implementation. Furthermore, we discuss our setup - a stage-gate process, where each location takes care of a different phase - and report occurred problems and how they supported or interfered with our teaching intentions.
Sensing Exocytosis and Triggering Endocytosis at Synapses: Synaptic Vesicle Exocytosis–Endocytosis Coupling

The intact synaptic structure is critical for information processing in neural circuits. During synaptic transmission, rapid vesicle exocytosis increases the size of never terminals and endocytosis counteracts the increase. Accumulating evidence suggests that SV exocytosis and endocytosis are tightly connected in time and space during SV recycling, and this process is essential for synaptic function and structural stability. Research in the past has illustrated the molecular details of synaptic vesicle (SV) exocytosis and endocytosis; however, the mechanisms that timely connect these two fundamental events are poorly understood at central synapses. Here we discuss recent progress in SV recycling and summarize several emerging mechanisms by which synapses can “sense” the occurrence of exocytosis and timely initiate compensatory endocytosis. They include Ca2+ sensing, SV proteins sensing, and local membrane stress sensing. In addition, the spatial organization of endocytic zones adjacent to active zones provides a structural basis for efficient coupling between SV exocytosis and endocytosis. Through linking different endocytosis pathways with SV fusion, these mechanisms ensure necessary plasticity and robustness of nerve terminals to meet diverse physiological needs.
Tryptophan catabolism and vitamin B-6 status are affected by gender and lifestyle factors in healthy young adults.

BACKGROUND Abnormalities of tryptophan (Trp) metabolism through the kynurenine (Kyn) pathway have been reported in various diseases; however, nutritional and lifestyle factors that affect this pathway in healthy individuals are not well documented. OBJECTIVE Our aim was to examine the effect of vitamin B-6 status and lifestyle factors including the use of vitamin B-6 supplements, alcohol, smoking, and oral contraceptives on Trp and its Kyn metabolites in a cohort of 2436 healthy young adults aged 18-28 y. METHODS Anthropometric and lifestyle data were collected by questionnaire. Participants provided blood samples for analysis of Trp, Kyn, anthranilic acid, kynurenic acid (KA), 3-hydroxykynurenine (HK), 3-hydroxyanthranilic acid (HAA), and xanthurenic acid (XA). Vitamin B-6 species were also measured. RESULTS Serum Trp metabolites were 10-15% higher among men (n = 993) compared with women (n = 1443; P < 0.0001), except for HK and XA. In all participants, serum Trp was positively associated with plasma pyridoxal 5'-phosphate (PLP; r = 0.28, P < 0.0001), reaching a plateau at PLP concentrations of ∼83 nmol/L. HK was inversely associated with PLP (r = -0.14, P < 0.01). Users of vitamin B-6 supplements (n = 671) had 6% lower concentrations of HK than nonusers (n = 1765; P = 0.0006). Oral contraceptive users (n = 385) had lower concentrations of KA (20.7%) but higher XA (24.1%) and HAA (9.0%) than did nonusers (n = 1058; P < 0.0001). After adjustment for gender and other lifestyle variables, XA concentrations were 16% higher in heavy drinkers (n = 713) than in never or occasional drinkers (n = 975; P = 0.0007). Concentrations of 2 other essential amino acids, methionine and arginine, also were positively associated with serum Trp (r = 0.65 and 0.33, respectively; P < 0.0001). CONCLUSIONS In this population of healthy young adults, gender has the largest influence on serum Kyn metabolite concentrations. The significant covariance of Trp with unrelated amino acids suggests that protein intake may be an important consideration in evaluating Kyn metabolism.
Three dimensional reconstruction of energy stores for jumping in planthoppers and froghoppers from confocal laser scanning microscopy

Jumping in planthopper and froghopper insects is propelled by a catapult-like mechanism requiring mechanical storage of energy and its quick release to accelerate the hind legs rapidly. To understand the functional biomechanics involved in these challenging movements, the internal skeleton, tendons and muscles involved were reconstructed in 3-D from confocal scans in unprecedented detail. Energy to power jumping was generated by slow contractions of hind leg depressor muscles and then stored by bending specialised elements of the thoracic skeleton that are composites of the rubbery protein resilin sandwiched between layers of harder cuticle with air-filled tunnels reducing mass. The images showed that the lever arm of the power-producing muscle changed in magnitude during jumping, but at all joint angles would cause depression, suggesting a mechanism by which the stored energy is released. This methodological approach illuminates how miniaturized components interact and function in complex and rapid movements of small animals. DOI: http://dx.doi. org/10.7554/eLife.23824. 001
Flavor Profile of Chinese Liquor Is Altered by Interactions of Intrinsic and Extrinsic Microbes

ABSTRACT The flavor profile of Chinese liquor is the result of the metabolic activity of its microbial community. Given the importance of the microbial interaction, a novel way to control the liquor's flavor is by regulating the composition of the community. In this study, we efficiently improved the liquor's flavor by perturbing the intrinsic microbial metabolism with extrinsic microbes. We first constructed a basic microbial group (intrinsic) containing Saccharomyces cerevisiae, Wickerhamomyces anomalus, and Issatchenkia orientalis and added special flavor producers (extrinsic), Saccharomyces uvarum and Saccharomyces servazzii, to this intrinsic group. Upon the addition of the extrinsic microbes, the maximum specific growth rates of S. cerevisiae and I. orientalis increased from 6.19 to 43.28/day and from 1.15 to 14.32/day, respectively, but that of W. anomalus changed from 1.00 to 0.96/day. In addition, most volatile compounds known to be produced by the extrinsic strains were not produced. However, more esters, alcohols, and acids were produced by S. cerevisiae and I. orientalis. Six compounds were significantly different by random forest analysis after perturbation. Among them, increases in ethyl hexanoate, isobutanol, and 3-methylbutyric acid were correlated with S. cerevisiae and I. orientalis, and a decrease in geranyl acetone was correlated with W. anomalus. Variations in ethyl acetate and 2-phenylethanol might be due to the varied activity of W. anomalus and S. cerevisiae. This work showed the effect of the interaction between the intrinsic and extrinsic microbes on liquor flavor, which would be beneficial for improving the quality of Chinese liquor.
ASAP Top-k Query Processing in Unstructured P2P Systems

Top-k query processing techniques are useful in unstructured peer-to-peer (P2P) systems, to avoid overwhelming users with too many results. However, existing approaches suffer from long waiting times. This is because top-k results are returned only when all queried peers have finished processing the query. As a result, query response time is dominated by the slowest queried peer. In this paper, we address this users' waiting time problem. For this, we revisit top-k query processing in P2P systems by introducing two novel notions in addition to response time: the stabilization time and the cumulative quality gap. Using these notions, we formally define the as-soon-as-possible (ASAP) top-k processing problem. Then, we propose a family of algorithms called ASAP to deal with this problem. We validate our solution through implementation and extensive experimentation. The results show that ASAP significantly outperforms baseline algorithms by re- turning final top-k result to users in much better times
Embodisuit: a wearable platform for embodied knowledge

The Embodisuit allows its wearer to map signals onto different places on their body. Informed by embodied cognition, the suit receives signals from an IoT platform, and each signal controls a different haptic actuator on the body. Knowledge is experienced ambiently without necessitating the interpretation of symbols by the conscious mind. The suit empowers wearers to reconfigure the boundaries of their selves strengthening their connection to the people, places, and things that are meaningful to them. It both critiques and offers an alternative to current trends in wearable technology. Most wearables harvest data from their users to be sent and processed elsewhere. The Embodisuit flips this paradigm such that data is taken in through the body instead. Furthermore, we believe that by changing the way people live with data, it will change the type of data that people create.
In Vitro Susceptibility of Ciprofloxacin-Resistant Methicillin-Resistant Staphylococcus aureus to Ototopical Therapy

Objective Despite the rising incidence of methicillin-resistant Staphylococcus aureus (MRSA) otologic infections, choice of treatment remains controversial. Only fluoroquinolone-containing ototopical preparations are approved by the US Food and Drug Administration for middle ear application. Furthermore, American Academy of Otolaryngology–Head and Neck Surgery Foundation guidelines advocate ototopical monotherapy for both tympanostomy tube otorrhea and acute otitis externa. Unfortunately, MRSA may be ciprofloxacin resistant. This causes confusion regarding antibiotic selection, because susceptibility profiles reflect a minimum inhibitory concentration (MIC), referenced against systemic, not ototopical, drug delivery dosing. The goal of this study is to determine the ciprofloxacin MIC for ciprofloxacin-resistant MRSA isolates from otologic infections and compare that value to the expected drug concentration achieved by fluoroquinolone ear drops and determine MRSA genotype for each isolate. Study Design In vitro assay with retrospective medical record review. Setting Tertiary care university hospital. Subjects and Methods Thirty otologically sourced ciprofloxacin-resistant MRSA isolates collected from adult and pediatric patients. MICs were calculated by broth dilution method. Isolates underwent multilocus sequence typing and polymerase chain reaction for arcA and Panton-Valentine leukocidin to establish the genotype. Results MICs ranged from 16 to 1025 µg/mL. There was a relationship between MIC and genotype; of the 7 isolates with an MIC value greater than 512 µg/mL, 6 were sequence type (ST)8. Conclusion These findings support the practice of ototopical monotherapy for patients with uncomplicated ciprofloxacin-resistant MRSA otitis externa. However, they raise concern that ototopical therapy may not be adequate to treat highly resistant strains of MRSA infecting the middle ear space.
Observations of central toroidal rotation in ICRF heated Alcator C-Mod plasmas

Impurity toroidal rotation has been observed in the centre of Alcator C-Mod ion cyclotron range of frequencies (ICRF) heated plasmas, from the Doppler shifts of argon X ray lines. Rotation velocities greater than 1.2 × 107 cm/s (ω = 200 krad/s) in the co-current direction have been observed in H mode discharges that had no direct momentum input. There is a correlation between the increase in the central impurity rotation velocity and the increase in the plasma stored energy (confinement enhancement), induced by ICRF heating, although other factors may be at play. The toroidal rotation velocity is highest near the magnetic axis, and decreases with increasing minor radius. A radial electric field of 300 V/cm at r/a = 0.3 has been inferred from the force balance equation. The direction of the rotation changes when the plasma current direction is reversed, remaining co-current. Impurity toroidal rotation in ICRF heated plasmas is in the direction opposite to the rotation in ohmic L mode plasmas; co-current rotation has also been observed during purely ohmic H modes. When the ICRF heating is turned off, the toroidal rotation decays with a characteristic time of order 50 ms, similar to the energy confinement time, and much shorter than the calculated neoclassical momentum damping time.
The limits of SDP relaxations for general-valued CSPs

It has been shown that for a general-valued constraint language Γ the following statements are equivalent: (1) any instance of VCSP(Γ) can be solved to optimality using a constant level of the Sherali-Adams LP hierarchy; (2) any instance of VCSP(Γ) can be solved to optimality using the third level of the Sherali-Adams LP hierarchy; (3) the support of Γ satisfies the “bounded width condition”, i.e., it contains weak near-unanimity operations of all arities.
The Vaccine Candidate Substrate Binding Protein SBP2 Plays a Key Role in Arginine Uptake, Which Is Required for Growth of Moraxella catarrhalis

ABSTRACT Moraxella catarrhalis is an exclusively human pathogen that is an important cause of otitis media in children and lower respiratory tract infections in adults with chronic obstructive pulmonary disease. A vaccine to prevent M. catarrhalis infections would have an enormous global impact in reducing morbidity resulting from these infections. Substrate binding protein 2 (SBP2) of an ABC transporter system has recently been identified as a promising vaccine candidate antigen on the bacterial surface of M. catarrhalis. In this study, we showed that SBP1, -2, and -3 individually bind different basic amino acids with exquisite specificity. We engineered mutants that each expressed a single SBP from this gene cluster and showed in growth experiments that SBP1, -2, and -3 serve a nutritional function through acquisition of amino acids for the bacterium. SBP2 mediates uptake of arginine, a strict growth requirement of M. catarrhalis. Adherence and invasion assays demonstrated that SBP1 and SBP3 play a role in invasion of human respiratory epithelial cells, consistent with a nutritional role in intracellular survival in the human respiratory tract. This work demonstrates that the SBPs of an ABC transporter system function in the uptake of basic amino acids to support growth of M. catarrhalis. The critical role of SBP2 in arginine uptake may contribute to its potential as a vaccine antigen.
Diabetes Self-Management in African Americans: An Exploration of the Role of Fatalism

PURPOSE This study was conducted to explore the concept of fatalism in relation to diabetes self-management behavior in African Americans with type 2 diabetes. METHODS Participants (n=39) were recruited from a clinic sample of African Americans with type 2 diabetes. Seven focus groups were conducted; the sessions were recorded, transcribed, and analyzed to identify themes related to fatalism and diabetes self-management. The ISAS paradigm (individual, symbols, audience, situation), a social psychology theory, provided the theoretical framework for the study. RESULTS Four dimensions of fatalism were identified: the meaning of diabetes, the illness experience, the individual's coping response, and the individual's religious and spiritual beliefs. For the participants in this study, fatalism seemed to characterize the nature of the interaction between the individual with diabetes and others, the meanings they attached to such interactions, and the decision to adopt an effective or ineffective diabetes self-management behavior. CONCLUSIONS Fatalism was associated with diabetes self-management in African Americans with diabetes and was multidimensional in this population; the construct appeared to differ conceptually from the perspective of current measures.
Analysis of Heritability Using Genome‐Wide Data

Most analyses of genome‐wide association data consider each variant independently without considering or adjusting for the genetic background present in the rest of the genome. New approaches to genome analysis use representations of genomic sharing to better account for confounding factors like population stratification or to directly approximate heritability through the estimated sharing of individuals in a dataset. These approaches use mixed linear models, which relate genotypic sharing to phenotypic sharing, and rely on the efficient computation of genetic sharing among individuals in a dataset. This unit describes the principles and practical application of mixed models for the analysis of genome‐wide association study data. © 2016 by John Wiley & Sons, Inc.
Case Series: Intrathecal Baclofen Therapy in Stiff‐Person Syndrome

Stiff‐person syndrome (SPS) is associated with axial rigidity superimposed on sustained muscle spasms. These symptoms commonly interfere with the performance of activities of daily living including ambulation. This retrospective case series evaluates the outcomes of screening tests and chronic infusion of intrathecal baclofen (ITB) in patients diagnosed with SPS treated in our spasticity clinic.
Zika virus like particles elicit protective antibodies in mice

Mosquito-borne Zika virus (ZIKV) typically causes a mild and self-limiting illness known as Zika fever. Since its recent emergence in 2014 in the American continent, ZIKV infection during pregnancy has been closely associated with a wide range of congenital abnormalities. To date, no vaccines or antivirals are publicly available. We developed Zika virus-like particles (VLPs) and evaluated their immunogenicity and protective efficacy in mouse models. ZIKV VLPs (ZIKVLPs) formulated with alum were injected into 6-8-week-old interferon deficient AG129 mice as well as wild type BALB/c mice. Control mice received PBS/alum. Animals were challenged with 200 PFU (>1000 AG129 LD50s) of ZIKV strain H/PF/2013. All vaccinated mice survived with no morbidity or weight loss while control animals either died at 9 days post challenge (AG129) or had increased viremia (BALB/c). Neutralizing antibodies were observed in all ZIKVLP vaccinated mice. The role of neutralizing antibodies in protecting mice was demonstrated by passive transfer. Our findings demonstrate the protective efficacy of the ZIKVLP vaccine and highlight the important role that neutralizing antibodies play in protection against ZIKV infection.