Miracle-dz/UniFAR-FTUs huggingface dataset:
Interfacing ultracold atoms with nanomagnetic domain walls

This thesis presents the first realisation of a new type of hybrid quantum device based on spintronic technology. We demonstrate an interaction between the magnetic fringing fields produced by domain walls within planar permalloy nanowires and a cloud of ultracold Rubidium 87 atoms. This interaction is manifested through the realisation of a magnetic atom mirror produced by a two-dimensional domain wall array. The interaction is tuned through the reconfiguration of the micromagnetic structure. Analytic modelling of the fringing fields is developed and shows good agreement with calculations based on micromagnetically simulated structures. The accurate and rapid calculation of the fringing fields permits simulation of the resulting atom dynamics, which agrees well with data. In turn, we use the atom dynamics as a probe of the micromagnetic reconfiguration processes that take place and observe a collective behaviour which is both reliably reproducible and in agreement with alternative, conventional magnetometry. We also observe evidence of stochastic behaviour, characteristic of superparamagnetic systems. We consider the development of a more advanced spintronics-based atom chip which will allow for the creation of extremely tight mobile atom traps. We consider the problems associated with ensuring that the trapping potential is adiabatic, sufficiently deep, and technically feasible. In particular we examine techniques to circumvent losses due to Majorana spin-flip transitions. As a result of this study we propose a novel scheme for creating time-averaged potentials via the piezoelectric actuation of magnetic field sources. We show that this technique presents significant fundamental and technical advantages over conventional time-averaging schemes.
Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens

Abstract Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.
Managing uncertainty: a qualitative study of GPs’ views on the diagnosis and immediate management of transient ischaemic attack and the potential of a diagnostic tool

Background Most patients with transient ischaemic attack (TIA) present to their GP. Early identification and treatment reduces the risk of subsequent stroke and consequent disability and mortality. Objective To explore GPs' views on the diagnosis and immediate management of suspected TIA, and the potential utility of a diagnostic tool. Methods This is a qualitative interview study based in Leicestershire, UK. A purposive sample of 10 GPs participated in 30-minute semi-structured telephone interviews. Data were analysed thematically. Results GPs reported that TIA was more likely to be suspected when patients were more obvious candidates for TIA based on their history, characteristics and symptom presentation. Referrals were in part a strategy to manage risk under conditions of uncertainty and to seek reassurance. GPs valued using a TIA risk stratification tool but felt this did not inform their diagnostic decision making. A diagnostic tool for TIA in primary care was seen to have potential to improve the decision-making process about diagnosis and management and enhance confidence of GPs, particularly in ruling out TIAs. GPs saw benefits of using hard thresholds, but remained concerned about missing TIAs and saw a tool as an adjunct to clinical judgement. Conclusions GPs weigh up the likelihood of TIA in the context of assessments of candidacy and diverse, often vague, symptoms. A diagnostic tool could support GPs in this process and help reduce reliance on referrals to TIA clinics for reassurance, provided the tool was designed to support decision making in cases of less 'typical' presentations.
Activation of an LPMO9 by an AA12 The pyrroloquinoline-quinone dependent pyranose dehydrogenase from Coprinopsis 1 cinerea ( Cc PDH) drives lytic polysaccharide monooxygenase (LPMO) action

19 Fungi secrete a set of glycoside hydrolases and oxidoreductases, including lytic 20 polysaccharide monooxygenases (LPMOs), for the degradation of plant polysaccharides. LPMOs 21 catalyze the oxidative cleavage of glycosidic bonds after activation by an external electron 22 donor. So far, only flavin-dependent oxidoreductases (from the auxiliary activity family AA3) 23 have been shown to activate LPMOs. Here we present LPMO activation by a pyrroloquinoline- 24 quinone (PQQ)-dependent pyranose dehydrogenase (PDH) from Coprinopsis cinerea , Cc PDH, 25 the founding member of the recently discovered auxiliary activity family AA12. Cc PDH 26 contains a C-terminal family 1 carbohydrate binding module (CBM1), an N-terminal family 27 AA8 cytochrome domain, and a central AA12 dehydrogenase domain. We have studied the 28 ability of full length Cc PDH and its truncated variants to drive catalysis by two Neurospora 29 crassa LPMOs. The results show that Cc PDH indeed can activate the C1-oxidizing Nc LPMO9F 30 and the C4-oxidizing Nc LPMO9C, that this activation depends on the cytochrome domain, and 31 that the dehydrogenase and the LPMO reactions are strongly coupled. The two tested Cc PDH- 32 LPMO systems showed quite different efficiencies and this difference disappeared upon addition 33 of free PQQ acting as a diphenol/quinone redox mediator, showing that LPMOs differ when it 34 comes to their direct interactions with the cytochrome domain. Surprisingly, removal of the 35 CBM domain from Cc PDH had a considerable negative impact on the efficiency of the Cc PDH- 36 LPMO systems, suggesting that electron transfer in the vicinity of the substrate is beneficial. Cc PDH does not oxidize cello-oligosaccharides, which makes this enzyme a useful tool for 38 studying cellulose-oxidizing LPMOs.
Survey on the Etiological Profile of Bacterial Neonatal Sepsis in and Around Vellore

Neonatal mortality is a major problem in the developing and under developed countries around the world. The commonest cause of mortality in neonates is sepsis, accounting for about 30-50% of neonatal deaths in developing countries. The clinical syndrome of sepsis is characterized by systemic signs of circulatory compromise caused by invasion of the blood stream by bacteria in the first four weeks of life. The present survey was carried out to determine the etiological profile of neonatal septicaemia and to find out the susceptibility pattern of pathogens causing neonatal sepsis so as to provide anti biogram appropriately. The blood samples were collected from the patients who come to OPD, Government Vellore Medical College and Hospital, Adukkamparai with suspected symptoms. The samples were inoculated onto various media to isolate the organisms from the blood samples. The isolated organisms were subjected to biochemical test for their identification and identified as CONS, Klebsiella pneumonia , E. coli , Enterobacter sps. , Pseudomonas aeruginosa and Acinetobacter sps. The antibiogram of the isolates showed higher percentage of sensitivity to Cefazolin, Cotrimoxazole and Levofloxacin. This result suggests the specific drugs for appropriate treatment.
The role of R&D networks for exploitative and explorative regional knowledge creation

The beneficial effect of R&D networks on regional knowledge creation is widely undenied. They constitute essential means to create new knowledge through collaborative research efforts and enable access to new knowledge by bridging the way to region-external knowledge bases. However, we argue that the significance and strength of the effect differs for different modes of knowledge creation – exploitative and explorative – as well as for the quantity and quality of knowledge created. To explore these differences, we estimate a set of spatial autoregressive (SAR) models for European regions with varying network effects that are based on a region’s network centrality in the cross-region R&D network of the EU Framework Programme (FP). The results point consistently to a higher positive impact of reginal network centralities on explorative than exploitative knowledge creation. Moreover, the quantity and quality of newly created knowledge is found to be conversely affected by the regional network centralities considered. Interestingly, a high number of links (degree centrality) has in relative terms higher positive effects on the quality, rather than the pure quantity of knowledge outputs, while an authoritative network position is more conducive for increasing the quantity than the quality of knowledge.
Sentiment Analysis or Opinion Mining: A Review

Opinion Mining (OM) or Sentiment Analysis (SA) can be defined as the task of detecting, extracting and classifying opinions on something. It is a type of the processing of the natural language (NLP) to track the public mood to a certain law, policy, or marketing, etc. It involves a way that development for the collection and examination of comments and opinions about legislation, laws, policies, etc., which are posted on the social media. The process of information extraction is very important because it is a very useful technique but also a challenging task. That mean, to extract sentiment from an object in the web-wide, need to automate opinion-mining systems to do it. The existing techniques for sentiment analysis include machine learning (supervised and unsupervised), and lexical-based approaches. Hence, the main aim of this paper presents a survey of sentiment analysis (SA) and opinion mining (OM) approaches, various techniques used that related in this field. As well, it discusses the application areas and challenges for sentiment analysis with insight into the past researcher's works.
Computing Arbitrage-Free Yields in Multi-Factor Gaussian Shadow-Rate Term Structure Models

This paper develops a method to approximate arbitrage-free bond yields within a term structure model in which the short rate follows a Gaussian process censored at zero (a "shadow-rate model" as proposed by Black, 1995). The censoring ensures that model-implied yields are constrained to be positive, but it also introduces non-linearity that renders standard bond pricing formulas inapplicable. In particular, yields are not linear functions of the underlying state vector as they are in affine term structure models (see Piazzesi, 2010). Existing approaches towards computing yields in shadow-rate models suffer from high computational burden or low accuracy. In contrast, I show that the technique proposed in this paper is sufficiently fast for single-step estimation of a three-factor shadow-rate term structure model, and sufficiently accurate to evaluate yields to within approximately half a basis point.
b Neutrophils Stimulated by IL-1 Protein Kinase Cascade in Human Selective Activation of p38 Mitogen-Activated

We investigated activation of mitogen-activated protein kinase (MAPK) subtype cascades in human neutrophils stimulated by IL-1 (cid:1) . IL-1 (cid:1) induced phosphorylation and activation of p38 MAPK and phosphorylation of MAPK kinase-3/6 (MKK3/6). Maximal activation of p38 MAPK was obtained by stimulation of cells with 300 U/ml IL-1 (cid:1) for 10 min. Extracellular signal-regulated kinase (ERK) was faintly phosphorylated and c-Jun N-terminal kinase (JNK) was not phosphorylated by IL-1 (cid:1) . IL-1 (cid:1) primed neutrophils for enhanced release of superoxide (O 2 (cid:2) ) stimulated by FMLP in parallel with increased phosphorylation of p38 MAPK. IL-1 (cid:1) also induced O 2 (cid:2) release and up-regulation of CD11b and CD15, and both responses were inhibited by SB203580 (p38 MAPK inhibitor), suggesting that p38 MAPK activation mediates IL-1 (cid:1) -induced O 2 (cid:2) release and up-regulation of CD11b and CD15. Combined stimulation of neutrophils with IL-1 (cid:1) and G-CSF, a selective activator of the ERK cascade, resulted in the additive effects when the priming effect and phosphorylation of p38 MAPK and ERK were assessed. IL-1 (cid:1) induced phosphorylation of ERK and JNK as well as p38 MAPK in human endothelial cells. These ﬁndings suggest that 1) in human neutrophils the MKK3/6-p38 aprotinin, and 10 (cid:2) g/ml leupeptin lysed for 60 min at 4°C. rapid centrifugation, the supernatant was mixed 1:1 with 2 (cid:2) sample buffer (4% SDS, 20% glycerol, 10% 2-ME, and a trace amount of bromphenol blue dye in 125 mM Tris-HCl, pH 6.8), heated at 100°C for 5 min, and then frozen at (cid:1) 80°C until use. Samples were subjected to 10% SDS gel elec-trophoresis. After electrophoresis, proteins were electrophoretically trans- ferred from the gel onto a nitrocellulose membrane in a buffer containing 25 mM Tris, 192 mM glycine and 20% methanol at 2 mA/cm 2 for 1.5 h at 25°C. Residual binding sites on the membrane was blocked by incubating the membrane in TBS (pH 7.6) containing 0.1% Tween 20 and 5% nonfat dry milk for 2 h at 25°C. The blots were washed in TBS containing 0.1% Tween 20 and then incubated with appropriate Ab overnight at 4°C. After washing, the membrane was incubated with anti-rabbit IgG Ab conjugated with HRP, and the Ab complexes were visualized by the ECL detection system as directed by the manufacturer. Endothelial cells were stimulated with cytokines for 10 min at 37°C. Cells were harvested using cell scraper and were resuspended in ice-cold extraction buffer. Endothelial cell extract was processed in the same manner described for neutrophils. Immunore- active bands quantiﬁed a NIH on a Macintosh
Pantropical modelling of forest functional traits using Sentinel-2 remote sensing data

Tropical forest ecosystems are undergoing rapid transformation as a result of changing environmental conditions and direct human impacts. However, we cannot adequately understand, monitor or simulate tropical ecosystem responses to environmental changes without capturing the high diversity of plant functional characteristics in the species-rich tropics. Failure to do so can result in oversimplified understanding of responses of ecosystems to environmental disturbances. Innovative methods and data products are needed to track changes in functional trait composition in tropical forest ecosystems through time and space. This study aimed to track key functional traits by coupling Sentinel-2 derived variables with a unique data set of precisely located in-situ measurements of canopy functional traits collected to a standardised methodology from field plots in countries spanning the four tropical continents (Australia, Brazil, Peru, Gabon, Ghana, and Malaysia). The spatial positions of individual trees above 10 cm DBH were mapped and their canopy size and shape recorded. From these data, community-level trait values were estimated at the same spatial resolution as Sentinel-2 imagery (i.e. 10m pixels). We use a geographical version of random forest to model and predict functional traits across our plots in the tropics. We demonstrate that key plant functional traits can be measured at a pantropical scale using the high spatial and spectral resolution of Sentinel-2 imagery in conjunction with climatic and soil related information. Pixel texture parameters were found to be key components of remote sensing information for predicting functional traits across tropical forests and woody savannas. Leaf thickness ( R 2 =0.52) obtained the highest prediction accuracy among the morphological and structural traits and leaf carbon content ( R 2 =0.70) and A max ( R 2 =0.67) obtained the highest prediction accuracy for leaf chemistry traits and photosynthesis related traits, respectively. Overall, the highest prediction accuracy was obtained for leaf chemistry and photosynthetic traits (A max and A sat ) in comparison to morphological and structural traits. Our approach offers new opportunities for mapping, monitoring and understanding biodiversity and ecosystem change in the most species-rich ecosystems on Earth. Modeling tropical montane forest biomass, productivity and canopy traits with multispectral remote sensing data.
lig a d M a r e :

Am J Psychiatry 169 :1 , January 2012 ajp.psychiatryonline. o rg 8 9 suffering is suggested by patterns of treatment utilization; nearly a quarter of people who seek help in any given year for a mental health problem do so from a clergy member, according to the National Comorbidity Survey (13). We had an opportunity to investigate the potential protective qualities of religiosity against major depression in a prospective design through an additional 10-year follow-up in which offspring of our original sample were interviewed in year 10 and year 20 (14). Overall, our initial findings showed that adult offspring of depressed as compared with nondepressed women were at high risk for lifetime major depression (14). Parental depression status determined high-risk status for offspring. In the additional follow-up period, we now have measures of religiosity and major depression at two points in time: at 10 years and at 20 years. In this study, our aim was to determine whether religiosity has a protective effect against depression, especially in the high-risk offspring. We ask two questions here: Does religiosity protect against major depression over 10 years in adults? If so, does this effect pertain equally to adults at high and low risk for ma(Am J P sych ia try 2 012 ; 1 69 :89–94 ) Re lig io sity and M a jo r D ep re ssion in A du lts a t H igh R isk : A Ten -Year P ro spe c tive S tudy
(2016). Modular analytical solutions for foundation damping in soil-structure interaction applications. Earthquake Spectra , 32 (3), 1749-1768.

Foundation damping incorporates combined effects of energy loss from waves propagating away from a vibrating foundation (radiation damping) and hysteretic action in supporting soil (material damping). Foundation damping appears in 8 analysis and design guidelines for force- and displacement-based analysis of 9 seismic building response (ASCE-7, ASCE-41), typically in graphical form 10 (without predictive equations). We derive closed-form expressions for foundation 11 damping of a flexible-based single degree-of-freedom oscillator from first 12 principles. The expressions are modular in that structure and foundation stiffness 13 terms, along with radiation and hysteretic damping ratios, appear as variables. 14 Assumptions inherent to our derivation have been employed previously, but the 15 present results are differentiated by: (1) the modular nature of the expressions; (2) 16 clearly articulated differences regarding alternate bases for the derivations and their 17 effects on computed damping; and (3) completeness of the derivations. Resulting 18 expressions indicate well-known dependencies of foundation damping on soil-to- 19 structure stiffness ratio, structure aspect ratio, and soil damping. We recommend a 20 preferred expression based on the relative rigor of its derivation.
A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly speciﬁc LAMP assay designed with comparative genomics

Molecular diagnostics of plant pathogens are crucial to prevent disease spread and to enhance food quality and security. A comparative genomics approach using genomes of different Xanthomonas species and pathovars was applied to identify highly speciﬁc targets in the genome of Xanthomonas fragariae , the causal agent of angular leaf spot of strawberry, listed under quarantine regulations in Europe. A reliable and sensitive loop-mediated isothermal ampliﬁcation (LAMP) assay was designed using a unique marker, providing a highly speciﬁc and rapid detection technique, convenient for on-site detection. Speciﬁcity of the designed assay was tested on 37 strains from a culture collection of X. fragariae , 82 strains of other Xanthomonas species and pathovars and 11 strains of other bacterial genera isolated from strawberry leaves. A detection limit of 10 2 fg was achieved, approximating to 20 genome copies per reaction. When performing analyses with crude plant material, a consistent lower detection efﬁciency of 10 2 CFU mL (cid:1) 1 was achieved. The LAMP assay designed in this study was adapted to work on crude plant material without any prior extensive extraction steps or incubation period; moreover, it does not require advanced analytical knowledge or a fully equipped laboratory. Results were produced within 7 – 20 min, depending on the pathogen concentration, thus providing a high-throughput and user-friendly method for detection and screening of plant material in support of quarantine regulations. leaf tissue the mix containing genomic DNA or lysed cells of X. fragariae , respectively. assays included a negative control, and a positive control with genomic DNA of X . fragariae LMG 25863.
TEACHING ARTIFICIAL INTELLIGENCE USING PROJECT-BASED LEARNING

This work presents an active learning methodology called Project-based learning (PBL) for developing artificial intelligence (AI) in a computer vision course of an undergraduate engineering degree. The objective of the course was to develop image recognition capabilities using Deep Learning (DL)/Machine Learning (ML) technics in real-world problems. The PBL learning methodology helped students search for real-world problems, develop complex solutions, and generate synergy among team members. The main role of the professor was to advise, guide and motivate the students throughout the course. The pedagogic innovation with active learning methodologies offered the professor the opportunity to create a dynamic motivating learning environment based on experiences. Each undergraduate engineering student had the opportunity to develop the skills and techniques of their profession: teamwork, proactivity, innovation, and leadership. The results obtained by the student teams showed problem-solving, including the use of automatic navigation equipment with AI, detection of the malaria parasite, recognition of non-human individuals to control vehicular traffic.
Refined Crystal Structure of Deoxyhemoglobin S I. RESTRAINED LEAST-SQUARES REFINEMENT AT 3.0-8, RESOLUTION*

The crystal stcucture of deoxyhemoglobin S has been refined at 3.0-A resolution using the Hendrickson-Konnert restrained least-squares method. Comparison with the structure of deoxyhemoglobin A reveals a hingelike movement of the @-chain A helices, which are involved in molecular contacts, toward the EF corners of their respective subunits. This movement brings the amino termini of the @-chains closer to the molecular dyad. The A helices remain a-helical throughout their entire lengths. No other major structural difference is found between deoxyhemoglobin A and deoxyhemoglobin S.