Miracle-dz/UniFAR-FTUs huggingface dataset:
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfill the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. Recent developments include the following. A community annotation project has been instigated in which acknowledged experts are invited to contribute summaries for peptidases. Software has been written to provide an Internet-based data entry form. Contributors are acknowledged on the relevant web page. A new display showing the intron/exon structures of eukaryote peptidase genes and the phasing of the junctions has been implemented. It is now possible to filter the list of peptidases from a completely sequenced bacterial genome for a particular strain of the organism. The MEROPS filing pipeline has been altered to circumvent the restrictions imposed on non-interactive blastp searches, and a HMMER search using specially generated alignments to maximize the distribution of organisms returned in the search results has been added.
Extensions to the support vector method

The Support Vector Machine (SVM) is a new technique for solving various function estimation problems. We refer to function estimation as learning, and a technique for estimating the unknown function from data as a learning machine. To construct a learning machine one requires four components: a domain (a learning problem with associated loss function), an induction principle, a set of decision functions, and nally an algorithm that implements all three other components. The present work is devoted to the extension of the Support Vector learning machine. Our objective is to show one can consider using the Support Vector approach in various contexts to solve various problems (in di erent domains, with di erent loss functions, induction principles and sets of decision functions). We argue that the Support Vector approach is a family of related algorithms that share some important common concepts and methodology { the approach is conceptually elegant and well supported by the theory. The material is organized as follows. We start with an introduction to the framework of statistical learning theory (Chapter 1). Chapter 2 describes the Support Vector approach and reviews achievements in the domains of pattern recognition, regression estimation and the solution of linear operator equations. The remainder of the work describes novel extensions to the Support Vector approach. Chapter 3 describes the extension of SVMs to the domain of multiclass pattern recognition, and Chapter 4 the extension of SVMs to the domain of density estimation. Chapter 5 introduces SVMs for pattern recognition which attempt to minimize leave{one{out error. Chapter 6 introduces SVMs with dictionaries of kernels for pattern recognition, regression estimation and density estimation. Chapter 7 introduces a method of transduction for function estimation. Finally, Chapter 8 concludes. 1
Agent-based Modeling of Social Conflict, Civil Violence and Revolution: State-of-the-art-review and Further Prospects

In this paper, we present a state-of-the-art review of Agent-based models (ABM) for simulation of social conflict phenomena, such as peaceful or violent street protests, civil violence and revolution. First, a simplified characterization of social conflict phenomena as emergent properties of a complex system is presented, together with a description of their macro and micro levels and the scales of the emergent properties. Then, existing ABM for simulation of crowd dynamics, civil violence and revolution are analyzed and compared, using a framework that considers their purpose/scope, environment representation, agent types and their architecture, the scales of the emergent properties, the qualitative and quantitative understanding of the phenomena provided by the results obtained from the models. We discuss the strengths and limitations of the existing models, as well as the promising lines of research for filling the gaps between the state-of-the-art models and real phenomena. This review is part of a work in progress on the assembling and dynamics of protests and civil violence, involving both simulation of the assembling process and the protest dynamics, as well as data collection in real protest events, and provides hints and guidelines for future developments.
Effect of Mechanical Stress on Cotton Growth and Development

Abstract Agricultural crops experience diverse mechanical stimuli, which may affect their growth and development. This study was conducted to investigate the effects of mechanical stresses caused by hanging labels from the flower petioles (HLFP) on plant shape and cotton yields in four cotton varieties: CCRI 41, DP 99B, CCRC 21, and BAI 1. HLFP significantly reduced plant height by between 7.8% and 36.5% in all four lines and also significantly reduced the number of fruiting positions per plant in the CCRI 41, DP 99B and CCRC 21 lines. However, the number of fruiting positions in BAI 1 was unaffected. HLFP also significantly reduced the boll weight for all four cultivars and the seed cotton yields for CCRI 41, DP 99B and BAI 1. Conversely, it significantly increased the seed cotton yield for CCRC 21 by 11.2%. HLFP treatment did not significantly affect the boll count in the fruiting branches of the 1st and 2nd layers in any variety, but did significantly reduce those on the 3rd and 4th fruiting branch layers for CCRI 41 and DP 99B. Similar trends were observed for the number of bolls per FP. In general, HLFP reduced plant height and boll weight. However, the lines responded differently to HLFP treatment in terms of their total numbers of fruiting positions, boll numbers, seed cotton yields, etc. Our results also suggested that HFLP responses might be delayed for some agronomy traits of some cotton genotypes, and that hanging labels from early-opening flowers might influence the properties related with those that opened later on.
Acute High-Altitude Illnesses

n engl j med 369;17 nejm.org october 24, 2013 1664 tion, the mice have normal body weight, adiposity, locomotor activity, and glucose homeostasis, similar to the findings in the patient. The data from these transgenic mice support the authors’ supposition that nonclassical regulation of estrogen receptor α is sufficient to protect against the obesity–metabolic syndrome phenotype associated with a total loss of activity of estrogen receptor α but is not sufficient to rescue the infertility phenotype. We offer the murine findings as support of the authors’ initial claims, and we believe these findings further implicate a differential role for classical versus nonclassical activity of estrogen receptor α in the regulation of energy and reproductive homeostasis.
Transformation of MDS/MPN‐RS‐T to AML: Trisomy 13, resistant thrombocytosis and transient disease control with oral busulfan therapy

body iron. Blood. 2003;101(9):3359–3364. [10] Cho JI, Basnyat B, Jeong C, et al. Ethnically Tibetan women in Nepal with low hemoglobin concentration have better reproductive outcomes. Evol Med Public Health. 2017;2017(1):82–96. [11] Norma T ecnica de Salud N8 134 para el manejo terap eutico y preventivo de la anemia en ni~ nos, adolescentes, mujeres gestantes y pu erperas RM 250-2017-MINSA. [12] Agrawal S, Berggren KL, Marks E, Fox JH. Impact of high iron intake on cognition and neurodegeneration in humans and in animal models: a systematic review. Nutr Rev. 2017;75(6):456–470.
The past, present, and future of telemedicine for Parkinson's disease

Travel distance, growing disability, and uneven distribution of doctors limit access to care for most Parkinson's disease (PD) patients worldwide. Telemedicine, the use of telecommunications technology to deliver care at a distance, can help overcome these barriers. In this report, we describe the past, present, and likely future applications of telemedicine to PD. Historically, telemedicine has relied on expensive equipment to connect single patients to a specialist in pilot programs in wealthy nations. As the cost of video conferencing has plummeted, these efforts have expanded in scale and scope, now reaching larger parts of the world and extending the focus from care to training of remote providers. Policy, especially limited reimbursement, currently hinders the growth and adoption of these new care models. As these policies change and technology advances and spreads, the following will likely develop: integrated care networks that connect patients to a wide range of providers; education programs that support patients and health care providers; and new research applications that include remote monitoring and remote visits. Together, these developments will enable more individuals with PD to connect to care, increase access to expertise for patients and providers, and allow more‐extensive, less‐expensive participation in research. © 2014 International Parkinson and Movement Disorder Society
Nitrate depletion and pH changes induced by the extraradical mycelium of the arbuscular mycorrhizal fungus Glomus intraradices grown in monoxenic culture.

The effect of the extraradical mycelium of the arbuscular mycorrhizal (AM) fungus Glomus intraradices Smith & Schenck on nitrate uptake and on the pH of the medium was studied in a monoxenic culture with tomato (Lycopersicon esculentum Mill. var. Vendor) roots obtained from root organ culture. The symbiosis was established in compartmented Petri dishes containing agar media amended with the pH indicator bromocresol purple. A pattern of pH changes was revealed as the symbiosis progressed in the media of the Petri dish compartments containing the dual, arbuscular-mycorrhizal fungi/root, culture as well as in the media of the hyphae, root-free compartments, in which the extraradical hyphae developed extensively, coming from the compartment containing the symbiosis. The colour changes in the media were measured spectrophotometrically, whilst maintaining the monoxenic conditions. The extraradical hyphae of G. intraradices strongly increased the pH of nutrient-free medium when supplied with nitrate, whereas the pH decreased m the absence of this N source. The hyphae developing from germinated spores and growing in axenic, nitrate-amended media did not induce any increase in pH. Nitrogen analysis revealed that a depletion of nitrate in the media accompanied increased pH. These results point towards an active uptake of nitrate by the extraradical mycelium of G. intraradices, probably coupled to a H+ -symport mechanism. The pH changes induced by AM fungal hyphae and the possible influence of the establishment of a functional symbiosis on these pH changes are discussed.
An Introduction to Quantum Computing

Preface 1. Introduction and background 2. Linear algebra and the Dirac notation 3. Qubits and the framework of quantum mechanics 4. A quantum model of computation 5. Superdense coding and quantum teleportation 6. Introductory quantum algorithms 7. Algorithms with super-polynomial speed-up 8. Algorithms based on amplitude amplification 9. Quantum computational complexity theory and lower bounds 10. Quantum error correction Appendices Bibliography Index
Translation and validation of Hindi version of Oral Health Impact Profile-14

Title of the Study: Validation of Hindi Version of Oral health Impact Profile (OHIP-14) Aim: To validate the Hindi version of OHIP-14. Settings and Design: The study was carried out in K.M. Shah Dental College & Hospital, Vadodara. Materials and Methods: OHIP-14 was translated into Hindi language.102 participants were given English as well as Hindi versions of OHIP-14. Statistical Analysis Used: Individual question were analyzed using Pearson Chi-Square test, Likelihood Ratio test and Linear-by-Linear Association test. The entire questionnaire in English and Hindi language were comparatively analyzed using Unpaired T test & Pearson correlation coefficient test. Results: All the 14 questions showed no statistically significant difference between the English OHIP-14 and the translated Hindi version of OHIP-14. Results of Unpaired T test (P = 0.61) were statistically insignificant. Pearson Correlation coefficient test was 0.963 suggesting that the translated Hindi version was highly correlated to the original English version. Conclusion: The translated Hindi version of OHIP-14 is hence established as a valid tool for conduction of oral health related & quality of life surveys in Hindi language which is the most commonly used language in the Indian subcontinent.
Designs of Plasmonic Metamasks for Photopatterning Molecular Orientations in Liquid Crystals

Aligning liquid crystal (LC) molecules into spatially non-uniform orientation patterns is central to the functionalities of many emerging LC devices. Recently, we developed a new projection photopatterning technique by using plasmonic metamasks (PMMs), and demonstrated high-resolution and high-throughput patterning of molecular orientations into arbitrary patterns. Here we present comparisons between two different types of metamask designs: one based on curvilinear nanoslits in metal films; the other based on rectangular nanoapertures in metal films. By using numerical simulations and experimental studies, we show that the PMMs based on curvilinear nanoslits exhibit advantages in their broadband and high optical transmission, while face challenges in mask designing for arbitrary molecular orientations. In contrast, the PMMs based on nanoapertures, though limited in optical transmission, present the great advantage of allowing for patterning arbitrary molecular orientation fields.
How contexts and issues influence the use of policy-relevant research syntheses: a critical interpretive synthesis.

CONTEXT Evidence briefs have emerged as a promising approach to synthesizing the best available research evidence for health system policymakers and stakeholders. An evidence brief may draw on systematic reviews and many other types of policy-relevant information, including local data and studies, to describe a problem, options for addressing it, and key implementation considerations. We conducted a systematic review to examine the ways in which context- and issue-related factors influence the perceived usefulness of evidence briefs among their intended users. METHODS We used a critical interpretive synthesis approach to review both empirical and nonempirical literature and to develop a model that explains how context and issues influence policymakers' and stakeholders' views of the utility of evidence briefs prepared for priority policy issues. We used a "compass" question to create a detailed search strategy and conducted electronic searches in CINAHL, EMBASE, HealthSTAR, IPSA, MEDLINE, OAIster (gray literature), ProQuest A&I Theses, ProQuest (Sociological Abstracts, Applied Social Sciences Index and Abstracts, Worldwide Political Science Abstracts, International Bibliography of Social Sciences, PAIS, Political Science), PsychInfo, Web of Science, and WilsonWeb (Social Science Abstracts). Finally, we used a grounded and interpretive analytic approach to synthesize the results. FINDINGS Of the 4,461 papers retrieved, 3,908 were excluded and 553 were assessed for "relevance," with 137 included in the initial sample of papers to be analyzed and an additional 23 purposively sampled to fill conceptual gaps. Several themes emerged: (1) many established types of "evidence" are viewed as useful content in an evidence brief, along with several promising formatting features; (2) contextual factors, particularly the institutions, interests, and values of a given context, can influence views of evidence briefs; (3) whether an issue is polarizing and whether it is salient (or not) and familiar (or not) to actors in the policy arena can influence views of evidence briefs prepared for that issue; (4) influential factors can emerge in several ways (as context driven, issue driven, or a result of issue-context resonance); (5) these factors work through two primary pathways, affecting either the users or the producers of briefs; and (6) these factors influence views of evidence briefs through a variety of mechanisms. CONCLUSIONS Those persons funding and preparing evidence briefs need to consider a variety of context- and issue-related factors when deciding how to make them most useful in policymaking.
Metapopulation dynamics in a changing climate: Increasing spatial synchrony in weather conditions drives metapopulation synchrony of a butterfly inhabiting a fragmented landscape

Habitat fragmentation and climate change are both prominent manifestations of global change, but there is little knowledge on the specific mechanisms of how climate change may modify the effects of habitat fragmentation, for example, by altering dynamics of spatially structured populations. The long‐term viability of metapopulations is dependent on independent dynamics of local populations, because it mitigates fluctuations in the size of the metapopulation as a whole. Metapopulation viability will be compromised if climate change increases spatial synchrony in weather conditions associated with population growth rates. We studied a recently reported increase in metapopulation synchrony of the Glanville fritillary butterfly (Melitaea cinxia) in the Finnish archipelago, to see if it could be explained by an increase in synchrony of weather conditions. For this, we used 23 years of butterfly survey data together with monthly weather records for the same period. We first examined the associations between population growth rates within different regions of the metapopulation and weather conditions during different life‐history stages of the butterfly. We then examined the association between the trends in the synchrony of the weather conditions and the synchrony of the butterfly metapopulation dynamics. We found that precipitation from spring to late summer are associated with the M. cinxia per capita growth rate, with early summer conditions being most important. We further found that the increase in metapopulation synchrony is paralleled by an increase in the synchrony of weather conditions. Alternative explanations for spatial synchrony, such as increased dispersal or trophic interactions with a specialist parasitoid, did not show paralleled trends and are not supported. The climate driven increase in M. cinxia metapopulation synchrony suggests that climate change can increase extinction risk of spatially structured populations living in fragmented landscapes by altering their dynamics.
Correlated lattice fermions in d

We show that even in d =~ dimensions the Hubbard model, when scaled properly, describes nontrivial correlations among fermions. Diagrammatic treatments are found to be substantially simpler than in Anite dimensions. The weak-coupling correlation energy is seen to be a good approximation for that in d=3. Recent approximations based on slave-boson techniques are recovered by the exact evaluation of explicit variational wave functions in d =~.
Preliminary analytical study on the feasibility of using reinforced concrete pile foundations for renewable energy storage by compressed air energy storage technology

Compressed air energy storage technology is one of the promising methods that have high reliability, economic feasibility and low environmental impact. Current applications of the technology are mainly limited to energy storage for power plants using large scale underground caverns. This paper explores the possibility of making use of reinforced concrete pile foundations to store renewable energy generated from solar panels or windmills attached to building structures. The energy will be stored inside the pile foundation with hollow sections via compressed air. Given the relatively small volume of storage provided by the foundation, the required storage pressure is expected to be higher than that in the large-scale underground cavern. The high air pressure typically associated with large temperature increase, combined with structural loads, will make the pile foundation in a complicated loading condition, which might cause issues in the structural and geotechnical safety. This paper presents a preliminary analytical study on the performance of the pile foundation subjected to high pressure, large temperature increase and structural loads. Finite element analyses on pile foundation models, which are built from selected prototype structures, have been conducted. The analytical study identifies maximum stresses in the concrete of the pile foundation under combined pressure, temperature change and structural loads. Recommendations have been made for the use of reinforced concrete pile foundations for renewable energy storage.
Metabolomic and proteomic analyses of a quiescent Escherichia coli cell factory reveal the mechanisms behind its production efficiency

Quiescent (Q-Cell) Escherichia coli cultures can be created by using the signalling molecule indole to halt cell division of an hns mutant strain. This uncouples metabolism from cell growth and allows for more efficient use of carbon feedstocks. However, the reason for the increased productivity of cells in this state was previously unknown. We show here that Q-cells can maintain metabolic activity in the absence of growth for up to 24 h, leading to four times greater per-cell productivity of a model metabolite, 3-hydroxybutyrate (3HB), than a control. Metabolomic data show that by disrupting the proton-motive force, indole interrupts the tricarboxylic acid cycle, leading to the accumulation of metabolites in the glycolysis pathway that are excellent starting points for high-value chemical production. By comparing protein expression patterns between wild-type and Q-cell cultures we show that Q-cells overexpress stress response proteins, which prime them to tolerate the metabolic imbalances incurred through indole addition. Quiescent cultures produced half the cell biomass of control cultures lacking indole, but were still able to produce 39.4 g.L-1 of 3HB compared to 18.6 g.L-1 in the control. Therefore, Q-cells have high potential as a platform technology for the efficient production of a wide range of commodity and high value chemicals.
Robula+: an algorithm for generating robust XPath locators for web testing

Automated test scripts are used with success in many web development projects, so as to automatically verify key functionalities of the web application under test, reveal possible regressions and run a large number of tests in short time. However, the adoption of automated web testing brings advantages but also novel problems, among which the test code fragility problem. During the evolution of the web application, existing test code may easily break and testers have to correct it. In the context of automated DOM‐based web testing, one of the major costs for evolving the test code is the manual effort necessary to repair broken web page element locators – lines of source code identifying the web elements (e.g. form fields and buttons) to interact with.
Antibacterial activity of 15-deoxygoyazensolide isolated from the stems of Minasia alpestris (Asteraceae) against oral pathogens

This work reports the isolation of the sesquiterpene lactone 15-deoxygoyazensolide from the stems of Minasia alpestris and the evaluation of its antimicrobial activity against the following oral pathogens: Enterococcus faecalis, Streptococcus salivarius, Streptococcus sobrinus, Streptococcus mutans, Streptococcus mitis, Streptococcus sanguinis, and Lactobacillus casei. Despite the cytotoxicity and genotoxicity of other sesquiterpene lactones of the furanoheliangolide-type, our results revealed that this compound exhibits low antibacterial activity against the evaluated oral pathogens; however, an interesting selectivity against E. faecalis (minimum inhibitory concentration [MIC] = 40 µg mL−1) and S. sobrinus (MIC = 60 µg mL−1) was observed.