Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid and sensitive detection ofStaphylococcus aureusin processed foods using a field‐deployed device to perform an insulated isothermal polymerase chain reaction‐based assay

Correspondence Hsiao-Wei Wen, Department of Food Science and Biotechnology, National Chung Hsing University, 145, Xingda Rd., Taichung 402, Taiwan, ROC. Email: hwwen@nchu.edu. tw Abstract This investigation we evaluated the feasibility of using the insulated isothermal polymerase chain reaction (iiPCR) reagent in a POCKIT system to detect Staphylococcus aureus in foods by comparing its results with those obtained using quantitative PCR (qPCR). The iiPCR/POCKIT system could specifically detect S. aureus and Staphylococcus spp. and differentiate them from 10 other foodborne pathogens. In a sensitivity analysis, the iiPCR/POCKITsystemhada100%(3/3)hit rate indetecting10–10CFU/mLS. aureus that had been spiked in skimmed milk. Three food samples that were spiked with 0.25 CFU/mL S. aureus—skimmed milk, vegetable mixture, and cooked chicken—yielded positive results following overnight enrichment. Finally, 24 food samples that were bought from traditional markets or convenience stores were tested. The iiPCR/POCKIT system and qPCR yielded the same results for 23 of the samples, excluding one papaya milk sample, indicating that the iiPCR/POCKIT system can be an effectiveway for the sensitive and automatic detection of S. aureus in various processed foods.
Tolerance to waterlogging in Parkia gigantocarpa Ducke saplings

Cette étude se propose d’évaluer les réponses biochimiques des arbrisseaux de Parkia gigantocarpa devant l’engorgement d’eau. L’engorgement est appliqué en inondant les arbrisseaux dans des pots de 14 kg jusqu’à approximativement 5 cm au-dessus de la surface du sol. Le plan expérimental a été façonné aléatoirement et comprenait deux types d’application de l’eau (contrôle et engorgement) sur cinq périodes d’évaluation (après 0, 4, 8, 12 et 16 jours d’engorgement), avec cinq réplications par traitement. Amidon, saccharose, hydrates de carbone solubles totaux et protéines solubles totales ont été mesurés. Les arbrisseaux soumis à engorgement ont montré des réductions significatives des concentrations d’amidon (62,50 %) et de protéines solubles totales (40,98 %), en particulier dans les feuilles. L’engorgement a réduit la concentration de saccharose dans les feuilles (44,38 %), tandis que cette concentration a augmenté dans les racines (76,78 %). La concentration d’hydrates de carbone solubles a augmenté de 106,9 % dans les racines des plantes exposées à l’engorgement. Cette étude a démontré la sensibilité des arbrisseaux de Parkia gigantocarpa à l’engorgement.
Denitrification inside the stratospheric vortex in the winter of 1999–2000 by sedimentation of large nitric acid trihydrate particles

[1] Synoptic-scale polar stratospheric clouds (PSCs) have been measured with an aircraft-borne lidar south of Spitsbergen in early February 2000. The PSCs of moderately depolarizing stratified layers extended from near the tropopause (10–11 km) up to 20 km altitude. Their internal structure in backscatter ratio reflects the variability of the particles' concentration rather than manifold sizes and phases of different optical efficiency. Actually, their size distribution was nearly monodisperse. According to T-matrix calculations, low backscatter ratios (γ < 3), color ratios of 1–1.5, and moderate depolarization ratios (δa ≈ 0.15–0.2) indicate that the observed layers were composed of aspherical nitric acid trihydrate (NAT) particles larger than 2 μm. During three turning point missions into the cold vortex core a significant settling of the particle layers was observed between aligned outgoing and incoming legs. Low stratospheric winds and quasi-Lagrangian flight heading minimized horizontal drifts between the probed volumes. A NAT particle sedimentation velocity of 69 ± 14 m/h is derived by cross-covariance analysis of corresponding pairs of two-dimensional backscatter sections of the layers. This implies a particle size of rp ≈ 7–8 μm and a mixing ratio of condensed HNO3 near 2 ppbv. The downward NOy flux below 19 km altitude amounts to j ≈ 3 ppbv km/d. Based on particle back trajectory analysis, this flux, derived from the observations in different regions of the Northern European Ice Sea, has a significant denitrification potential.
How Reliable are Prefrontal tDCS Effects – Zero–effects on the Keep–track Task?

Recent neuroimaging studies showed that in addition to the dorsolateral prefrontal cortex (dlPFC), the posterior parietal cortex (PPC) plays a significant role in higher cognitive processes such as executive functions. In this study we aimed to explore the neural underpinnings of executive function of updating by exploring the effects of transcranial direct current stimulation (tDCS) over dlPFC and PCC. Nineteen healthy right–handed participants took part in a cross–over sham–controlled experiment. All participants underwent three tDCS conditions (active tDCS over the left dlPFC; active tDCS over the left PPC; and sham) in counterbalanced order. Following tDCS participants completed the keep–track task, with parallel forms being used in different test–sessions. As a control measure, we used a choice reaction time task. Results showed no significant effects of tDCS regardless of the localization of stimulation. Our results are in contrast with results of other studies exploring prefrontal tDCS effects on updating and do not allow for deriving conclusions about the role of the left PPC in the ability to update information in working memory.
Co-occurrence of kdr mutations V1016I and F1534C in pyrethroid-resistant Aedes aegypti (Diptera: Culicidae) populations from Costa Rica

Aedes aegypti (Linnaeus, 1762) is considered the most important mosquito vector species for several arboviruses (e.g., dengue, chikungunya, Zika) in Costa Rica. The main strategy for the control and prevention of Aedes-borne diseases relies on insecticide-based vector control. However, the emergence of insecticide resistance in the mosquito populations present a big threat for the prevention actions. The characterization of the mechanisms driving the insecticide resistance in Ae. aegypti are vital for decision making in vector control programs. Therefore, we analyzed the voltage-gated sodium channel gene for the presence of the V1016I and F1534C kdr mutations in pyrethroid-resistant Ae. aegypti populations from Puntarenas and Limon provinces, Costa Rica. The CDC bottle bioassays showed that both Costa Rican Ae. aegypti populations were resistant to permethrin and deltamethrin. In the case of kdr genotyping, results revealed the co-occurrence of V1016I and F1534C mutations in permethrin and deltamethrin-resistant populations, as well as the fixation of the 1534C allele. Therefore, our findings make an urgent call to expand the knowledge about the insecticide resistance status and mechanisms in the Costa Rican populations of Ae. aegypti which must be a priority to develop an effective resistance management plan.
Transmission of Enteropathogens through Fresh Herbs and Method of using them as Safe Condiments

Background and objectives: As an indispensable dietary component, fresh fruits and vegetables, which are often consumed raw, have been reported to harbor large microbial populations often culminating in enteric disease outbreaks. The present study aimed to assess the microbial quality of coriander and mint and find the efficacy of potassium permanganate (KMnO 4) in effectively removing such microbes. Materials and methods: Ten grams each of fresh, unstored green coriander (n = 50) and mint (n = 50) samples were examined for their parasitic and bacterial content before and after washing with tap water and with an aqueous solution of 0.001% KMnO 4. The different species of bacteria, as well as their main burden in these herbs, were also estimated along with the parasites they harbored. Results: Only 22% unwashed herbs harbored parasites which were reduced to a significant number on washing with tap water. One hundred percent of the herb samples before washing, and 98% of tap water washed herb samples were contaminated with bacteria. A total of 33 different species of bacteria were isolated, from members of the family Enterobacteriaceae (56.3%) Pseudomonadaceae (15.6%) , Vibrionaceae (9.4%,) , and Acinetobacteriaceae (6.2%). These bacteria were significantly removed after treatment with KMnO 4 . Conclusion: The study reveals the presence of harmful enteric bacteria and parasites in fresh green coriander and mint which are liable to cause enteric diseases. We recommend that all the fresh produce which is consumed raw should be treated with 0.001% KMnO 4 after tap water washing to render them safe for consumption.
The fms 21 ( pilA )-fms 20 locus encoding one of four distinct pili of Enterococcus faecium

In the last two decades, enterococci, especially Enterococcus faecalis and Enterococcus faecium, have emerged as multidrug-resistant opportunistic pathogens causing difficult-to-treat healthcare-associated (HA) infections including endocarditis (Arias & Murray, 2009). Recent surveillances reported a major epidemiological shift of increasing frequency of isolation of E. faecium from United States hospitals (Hidron et al., 2008). Furthermore, increased morbidity and mortality due to vancomycin-resistant strains of E. faecium have also been reported in patients who have multiple medical problems, such as cancer, transplantation or prior surgery. Using multilocus sequence typing, epidemiological studies have shown that the HA E. faecium strains are different sequence types from the commensal strains that colonize the gastrointestinal tract of healthy humans (Top et al., 2008). Further analyses suggested that the recent success of the E. faecium hospital-associated genogroup [also referred to as clonal complex 17 (CC17); Top et al., 2008] is due at least in part to the presence of an active form of the acm gene encoding collagen adhesin (Nallapareddy et al., 2008) or acquisition of additional genetic loci encoding enterococcal surface protein (espfm) (Willems et al., 2001), a hyaluronidase-like glycoside hydrolase (hylEfm) (Rice et al., 2003) or E. faecium surface proteins (fms) (Hendrickx et al., 2007; Sillanpaa et al., 2008, 2009).
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

The usage made of protein surfaces by nucleic acids still remains largely unknown, due to the lack of available structural data and the inherent complexity associated to protein surface deformability and evolution. In this work, we present a method that contributes to decipher such complexity by predicting protein-DNA interfaces and characterizing their properties. It relies on three biologically and physically meaningful descriptors, namely evolutionary conservation, physico-chemical properties and surface geometry. We carefully assessed its performance on several hundreds of protein structures. We achieve a higher sensitivity compared to state-of-the-art methods, and similar precision. Importantly, we show that our method is able to unravel ‘hidden’ binding sites by applying it to unbound protein structures and to proteins binding to DNA via multiple sites and in different conformations. It is implemented as a fully automated tool, , freely accessible at: http://www.lcqb. upmc.fr/JET2DNA. We also provide a new reference dataset of 187 protein-DNA complex structures, representative of all types of protein-DNA interactions, along with a subset of associated unbound structures: http://www.lcqb. upmc.fr/PDNAbenchmarks.
A random effects stochastic block model for joint community detection in multiple networks with applications to neuroimaging

Motivated by multi-subject experiments in neuroimaging studies, we develop a modeling framework for joint community detection in a group of related networks, which can be considered as a sample from a population of networks. The proposed random effects stochastic block model facilitates the study of group differences and subject-specific variations in the community structure. The model proposes a putative mean community structure which is representative of the group or the population under consideration but is not the community structure of any individual component network. Instead, the community memberships of nodes vary in each component network with a transition matrix, thus modeling the variation in community structure across a group of subjects. To estimate the quantities of interest we propose two methods, a variational EM algorithm, and a model-free "two-step" method based on either spectral or non-negative matrix factorization (NMF). Our NMF based method Co-OSNTF is of independent interest and we study its convergence properties to a stationary point. We also develop a resampling-based hypothesis test for differences in community structure in two populations both at the whole network level and node level. The methodology is applied to a publicly available fMRI dataset from multi-subject experiments involving schizophrenia patients. Our methods reveal an overall putative community structure representative of the group as well as subject-specific variations within each group. Using our network level hypothesis tests we are able to ascertain statistically significant difference in community structure between the two groups, while our node level tests help determine the nodes that are driving the difference.
Antioxidant Activity of Phenolic Compounds from Different Grape Wastes

Winery pomace (from red and white grapes) was extracted under various conditions using different solvents. The antioxidant activity of solvent extracts was investigated by DPPH radical scavenging method. Ethanol extract exhibited the highest antioxidant activity compared to the other solvent (BuOH, EtOAc, Me2Cl2 and pet.ether). There was a correlation between antioxidant activity and total phenol content. HPLC analysis of the extracts showed that gallic and cinnamic acid was the major phenolic compounds in winery pomace. Various phenolic compounds such as catechin, rutin, rosmarinic, chlorogenic, caffeic, vanillic, coumaric acids were also identified.
Taxonomic and phylogenetic review of Necrosuchus ionensis (Alligatoroidea: Caimaninae) and the early evolution and radiation of caimanines

Alligatoroidea is the most species-rich crocodylomorph clade of the Cenozoic of South America, with nearly all species belonging to the Caimaninae clade. However, the earliest records of Caimaninae in South America, which are from the Palaeocene, are based mostly on incomplete specimens, which increases the importance of detailed taxonomic and phylogenetic studies on these taxa. This paper offers a taxonomic and phylogenetic review of Necrosuchus ionensis, a caimanine species from the Salamanca Formation of the Palaeocene of Argentina. Necrosuchus ionensis is considered a valid species, albeit with a different diagnosis from that proposed by previous authors. The phylogenetic analysis shows, for the first time, that N. ionensis belongs to the derived Caimaninae clade Jacarea. However, a better understanding of the Jacarea clade is needed, and alternative placements for N. ionensis might be considered. Nevertheless, the placement of N. ionensis as a derived caimanine raises interesting perspectives on the early evolution and radiation of caimanines, which are thoroughly discussed in this paper together with other results obtained in this study, such as the recovery of the North American caimanines Bottosaurus and Tsoabichi as a clade.
ADBI Working Paper Series STRUCTURAL CHANGE WITH PUBLIC EDUCATIONAL EXPENDITURE: EVIDENCE FROM THE PEOPLE’S REPUBLIC OF CHINA

This paper represents an early attempt to analyze the comprehensive relationship between public educational expenditure and structural change, which is often measured by labor transfer from agricultural sector to industrial sector in developing economies. I construct a two-sector general equilibrium model, showing that in the short term, public educational expenditure mainly crowds out industrial capital accumulation and thus temporarily hinders structural change, while there is an inverted-U relationship between them in the long run, as public educational expenditure helps reduce the educational cost of rural residents permanently. The People’s Republic of China’s (PRC) hukou system provides appropriate data to empirically identify this comprehensive relationship. The empirical evidence confirms the theoretical interpretations when I control for confounding factors, take the endogeneity of public educational expenditure into account, and investigate the mechanisms behind the relationship. The PRC’s current level of public educational expenditure is still far from its optimal value, as indicated by the inverted-U relationship with structural change, suggesting that the PRC should increase spending on public education, especially for rural residents.
Growth and Human Capital : A Network Approach ∗ Short Title : Growth , Human Capital and Networks

We study the interactions of human capital, growth and inequality by embedding networks into an endogenous growth model with overlapping generations. Human capital depends on investment in education and the average human capital of a household’s neighborhood. High network cohesion leads to long run equality, while for low network cohesion inequality is high and persists more often. During transition, high overall growth is achieved when the network has high degree centralization, and high individual growth is achieved when the household has low human capital relative to its neighborhood and is located in a neighborhood with high average human capital.
Counting the disabled: Using survey self-reports to estimate medical eligibility for social security's disability programs

This paper develops an approach for tracking medical eligibility for the Social Security Administration’s (SSA’s) disability programs on the basis of self-reports from an ongoing survey. Using a structural model of the disability determination process estimated on a sample of applicants, we make out-of-sample predictions of eligibility for nonbeneficiaries in the general population. This work is based on the 1990 panel of the Survey of Income and Program Participation. We use alternative methods of estimating the number of people who would be found eligible if they applied, considering the effects of sample selection adjustments, sample restrictions, and several methods of estimating eligibility/ineligibility from a set of continuous probabilities. The estimates cover a wide range, suggesting the importance of addressing methodological issues. In terms of classification rates for applicants, our preferred measure outperforms the conventional single variable model based on the “prevented” measure. Under our preferred estimate, we find that 4.4 million people2.9 percent of the nonbeneficiary population aged 18-64would meet SSA’s medical criteria for disability. Of that group, about one-third have average earnings above the substantial gainful activity limit. Those we classify as medically eligible are similar to allowed applicants in terms of standard measures of activity limitations.
First record of Labeo capensis (Smith, 1841) in the Crocodile River (West) system: another successful non-native freshwater fish introduction in South Africa

South Africa is one of six global fish invasion hotspots and as a result, non-native fishes are common components of the fish assemblages in all of the major river systems. The rate of establishment for introduced fish into South African rivers is high (79%) and the vector responsible for the highest establishment rate is interbasin transfer schemes with 80%. Introductions of non-native fish into river systems can negatively affect native fish species through hybridisation, competition for food sources and predation, and the introduction of associated parasites and diseases. The aims of the current study were to provide evidence of the introduction of Labeo capensis into the Crocodile River (West) system, using morphological and molecular techniques, and to record the fish health and gonadosomatic index to determine the invasive status of L. capensis. From the fish health assessment index and gonadosomatic index of L. capensis collected from Olifantsnek Dam, it can be concluded that L. capensis is a healthy reproducing population. Because this fish species can survive and reproduce in newly colonised river systems, it has the potential to compete with the native fish species for food and habitat, but can also hybridise with native Labeo species.
LOWER LIMB JOINT AND MUSCLE FORCES DURING SLOPED WALKING AT SELFSELECTED SPEED

The aim of this study was to analyse lower limb joint and muscle forces during level and sloped walking. Male participants (n=18, 27+-5 y, 1.80+-0.05 m, 75+-8 kg) walked at -speed at level and on a ramp (+-18"). Joint and muscle forces were analysed using a musculoskeletal model. Downhill walking increased maximum tibiofemoral and patellofemoral compression forces and decreased ankle compression forces, while uphill walking increased all analysed lower limb joint forces. Muscle forces were altered during sloped walking. Amongst others, downhill walking increased quadriceps (>248%) and decreased gastrocnemii (less than 63%) muscle forces in comparison to level walking. Uphill walking increased mean quadriceps (>57%) and gastmnemii (>40%) muscle forces. Results might be used for the development of rehabilitation and training procedures.
Optimizing the design of a plug-in hybrid electric vehicle from the early phase: an advanced sizing methodology

ABSTRACTA plug-in hybrid electric powertrain, as one of the most promising solutions to increase the fuel economy and to meet the stringent requirements of low emissions urban zones, has been investigated and developed for a light duty commercial vehicle application in this work. The plug-in hybrid electric powertrain combines an advanced small diesel internal combustion engine with a high energy battery pack, capable to assure an extended range in pure electric mode for specific areas, like the low/zero emissions urban zones. Since the right size of the powertrain components is essential to fully exploit the benefits of the hybridization, an advanced methodology has been proposed to optimize the design of the plug-in hybrid powertrain at an early phase. This methodology is based on the genetic algorithm approach for the choice of the powertrain component characteristics, combined with a quasi-optimal energy management strategy that is the Equivalent fuel Consumption Management Strategy (ECMS). The perfor.