Miracle-dz/UniFAR-FTUs huggingface dataset:
Ocean Reanalyses: Recent Advances and Unsolved Challenges

Ocean reanalyses combine ocean models, atmospheric forcing fluxes, and observations using data assimilation to give a four-dimensional description of the ocean. Metrics assessing their reliability have improved over time, allowing reanalyses to become an important tool in climate services that provide a more complete picture of the changing ocean to end users. Besides climate monitoring and research, ocean reanalyses are used to initialize sub-seasonal to multi-annual predictions, to support observational network monitoring, and to evaluate climate model simulations. These applications demand robust uncertainty estimates and fit-for-purpose assessments, achievable through sustained advances in data assimilation and coordinated inter-comparison activities. Ocean reanalyses face specific challenges: i) dealing with intermittent or discontinued observing networks, ii) reproducing inter-annual variability and trends of integrated diagnostics for climate monitoring, iii) accounting for drift and bias due e.g. to air-sea flux or ocean mixing errors, iv) optimizing initialization and improving performances during periods and in regions with sparse data. Other challenges such as multi-scale data assimilation to reconcile mesoscale and large-scale variability and flow-dependent error characterization for rapidly evolving processes, are amplified in long-term reanalyses. The demand to extend reanalyses backward in time requires tackling all these challenges, especially in the emerging context of earth system reanalyses and coupled data assimilation. This mini-review aims at documenting recent advances from the ocean reanalysis community, discussing unsolved challenges that require sustained activities for maximizing the utility of ocean observations, supporting data rescue and advancing specific research and development requirements for reanalyses.
Reasons for Women's Choice of Elective Caesarian Section in Duayaw Nkwanta Hospital

Background Caesarean section is one of the most commonly performed major surgeries in obstetric practice intended to save the mother and child and in turn reduce maternal and perinatal mortality. The steadily increasing global rate of caesarean section has become one of the most debated topics in maternity care. This study identified the factors that influence women's choice of elective cesarean sections in the Duayaw Nkwanta Hospital. Methodology This study used descriptive cross-sectional survey method to collect data from 78 post-caesarean section women above age 18 years. A whole population sampling method was used to trace respondents to their homes to administer a pretested questionnaire. Data was double-entered into Microsoft Excel spreadsheet, compared, cleaned, and transported to Statistical Package for Social Sciences (SPSS) version 21. Data was analyzed using descriptive statistics with a Pearson correlation test. Results Post-caesarean section women (37.2%) indicated CS is a pain-free method of birth while 57.1% reported CS is safe for both mother and baby. Others (28.2%) chose CS based on a friend's advice and 19.2% on religious advice. The relationship between age of respondents and the number of times of having CS showed a weak positive correlation (r= .170, N= 78, p≤0.136, two-tailed test). There was a significant positive correlation between average monthly income of respondents and the number of times of having a CS birth (r= .320, N= 78, p≤ 0.004). Conclusion It is imperative that there is heightened interest in educating mothers on associated benefit and risk of elective caesarean sections as a method of birthing by nurses and midwives in the antenatal clinics.
Meiotic drive reduces egg-to-adult viability in stalk-eyed flies

SR meiotic drive is a selfish genetic element located on the X chromosome in a number of species that causes dysfunction of Y-bearing sperm. SR is transmitted to up to 100% of offspring, causing extreme sex ratio bias. SR in several species is found in a stable polymorphism at a moderate frequency, suggesting there must be strong frequency-dependent selection resisting its spread. We investigate the effect of SR on female and male egg-to-adult viability in the Malaysian stalk-eyed fly, Teleopsis dalmanni. SR meiotic drive in this species is old, and appears to be broadly stable at a moderate (~20%) frequency. We use large-scale controlled crosses to estimate the strength of selection acting against SR in female and male carriers. We find that SR reduces the egg-to-adult viability of both sexes. In females, homozygous females experience greater reduction in viability (sf = 0.242) and the deleterious effects of SR are additive (ℎ = 0.511). The male deficit in viability (sm = 0.214) is not different from that in homozygous females. The evidence does not support the expectation that deleterious side-effects of SR are recessive or sex-limited. We discuss how these reductions in egg-to-adult survival, as well as other forms of selection acting on SR, act to maintain SR polymorphism in this species.
Effect of betaine and ascorbic acid in drinking water on growth performance and blood biomarkers in meat ducks exposed to heat stress

The aim of this study was to compare the effect of drinking water that contains various levels of ascorbic acid (AA) and betaine (BT) on growth performance and blood biomarkers in meat ducks exposed to heat stress. Six hundred and forty one-day-old Cherry Valley ducks were randomly assigned to one of seven treatment groups: i) control group, drinking water without ascorbic acid or betaine, ii) AA100, drinking water containing ascorbic acid at 100 milligrams per litre, iii) AA200, drinking water containing ascorbic acid at 200 milligrams per litre, iv) AA300, drinking water containing ascorbic acid at 300 milligrams per litre, v) BT400, drinking water containing betaine at 400 milligrams per litre, vi) BT800, drinking water containing betaine at 800 milligrams per litre, and vii) BT1200, drinking water containing betaine at 1200 milligrams per litre. The ducks were exposed to heat stress (11:00 to 17:00, 33 °C to 43 °C, relative humidity 70%, artificially controlled-environment houses) from the 22nd to 42nd days. Ducks from treatment groups AA300 and BT1200 displayed significantly increased bodyweight gains compared with those in the control group. Blood levels of glucose, and activities of aspartate aminotransferase and alanine aminotransferase in all treatment groups were significantly lower than those observed in the control group. Red blood cell count, platelet number, electrolytes and blood gas concentrations were significantly higher in all treatment groups compared with those in the control group. Blood pH levels in all treatment groups were lower than those in the control group. In conclusion, drinking water containing ascorbic acid or betaine improved the growth performance via biomarker homeostasis in blood of meat ducks exposed to heat stress. Keywords: body weight gain, blood lipid, red blood cell, electrolytes; blood gas, blood pH
Photoperiodic conditions as a factor modulating leptin influence
on pro-inflammatory cytokines
and their receptors gene expression in ewe’s aorta

Cardiovascular diseases (CVD) such as hypertension, ischemic heart or heart failure, are currently the leading cause of death worldwide. According to World Health Organization (WHO) statistics, in 2008 the number of deaths due to CVD was 17.3 mln, which accounted for nearly 30% of all deaths (WHO, 2011). The underlying cause of CVD is atherosclerosis which is a chronic inflammation state of the aorta and arteries of medium size (epicardial, coronary, carotid, renal, pelvic, mesenteric). Atherosclerosis can be however treated as ‘inflammation disease’ in two aspects. ABSTRACT. Atherosclerosis, a chronic inflammation state of the aorta, is characterised by increased levels of pro-inflammatory cytokines (tumour necrosis factor alpha (TNFα), interleukin (IL)-1β, IL-6). Sheep is used in both cardiovascular and immunological studies; besides, ‘long-day’ ewe can be a model of leptin resistance state. The aim of the study was to examine whether photoperiodic conditions (long-day (LD) and short-day (SD) seasons) are a key factor modulating exogenous leptin influence on pro-inflammatory cytokines and their receptors gene expression in aorta of ewe’s with or without prior induction of acute inflammation. The experiment was conducted on 48 ewes during SD and LD seasons which were randomly divided into 4 groups: control; with LPS injection (400 ng/kg of body weight (BW)); with leptin injection (20 μg/kg BW); and with LPS and 30-min later leptin injection. Three hours after LPS/control treatment animals were euthanized to collect the thoracic aorta samples. In both seasons leptin injection intensified LPS-induced increase in IL1B gene expression but only in SD season leptin injection increased IL1R1 and IL1R2 gene expressions. The leptin injection increased IL6 gene expression but only in SD season. In the LD season leptin enhanced the LPS effect on IL6 gene expression. Neither TNFA nor its receptors gene expression was influenced by leptin regardless of season. In the thoracic aorta tissue an exogenous leptin exerts effect on pro-inflammatory cytokines and their receptors gene expression; however in ewe this influence depends on photoperiodic conditions. Moreover, leptin can moderate progression of the inflammation reaction in this tissue. Received: 4 March 2019 Revised: 22 May 2019 Accepted: 17 June 2019
Mechanisms of MTOC clustering and spindle positioning in the budding yeast Cryptococcus neoformans: a microtubule grow-and-catch model

Mitotic spindle formation in the pathogenic budding yeast, Cryptococcus neoformans, depends on multitudes of inter-dependent interactions involving kinetochores (KTs), microtubules (MTs), spindle pole bodies (SPBs), and molecular motors. Before the formation of the mitotic spindle, multiple visible microtubule organizing centers (MTOCs), coalesce into a single focus to serve as an SPB. We propose a ‘grow-and-catch’ model, in which cytoplasmic MTs (cMTs) nucleated by MTOCs grow and catch each other to promote MTOC clustering. Our quantitative modeling identifies multiple redundant mechanisms mediated by a combination of cMT-cell cortex interactions and inter-cMT coupling to facilitate MTOC clustering within the physiological time limit as determined by time-lapse live-cell microscopy. Besides, we screened various possible mechanisms by computational modeling and propose optimal conditions that favor proper spindle positioning - a critical determinant for timely chromosome segregation. These analyses also reveal that a combined effect of MT buckling, dynein pull, and cortical push maintain spatiotemporal spindle localization. Author summary Cells actively self-assemble a bipolar spindle to facilitate chromosomal segregation. Multiple MTOCs, on the outer nuclear envelope, cluster into a single SPB before spindle formation during semi-open mitosis of the budding yeast Cryptococcus neoformans. Eventually, the SPB duplicates and organizes the spindle to position it within the daughter bud near the septin ring during anaphase. In this work, we tested various computational models to match physiological phenomena in an attempt to find plausible mechanisms of MTOC clustering and spindle positioning in C. neoformans. Notably, we propose an MT ‘grow-and-catch’ model that relies on possible redundant mechanisms for timely MTOC clustering mediated by (a) minus end-directed motors that crosslink and slide anti-parallel cMTs from different MTOCs on the nuclear envelope and (b) a Bim1 mediated biased sliding of cMTs along the cell cortex toward the septin ring that pulls MTOCs in the presence of suppressed dynein activity. By combining an analytical model and stochastic MT dynamics simulations, we screened various MT-based forces to detect steady spindle positioning. By screening the outputs of various models, it is revealed that proper spindle positioning near the septin ring requires MT buckling from the cell cortex.
Training systems and rootstocks on yield and agronomic performance of ‘Syrah’ grapevine in the Brazilian semiarid

ABSTRACT The Vale do São Francisco stands out among the main Brazilian wine regions, and ‘Syrah’ is a grape cultivar very important to produce red wines. The objective of this study was to evaluate the influence of training systems and rootstocks on the yield and other agronomic variables of ‘Syrah’ grapevines during eight consecutive harvests in the tropical semiarid environment in the Vale do São Francisco. An experiment was carried out in Petrolina, state of Pernambuco, with ‘Syrah’ trained to lyre and espalier systems and grafted on IAC 572, IAC 766, IAC 313, SO4, 1103 Paulsen and Harmony rootstocks. A randomized block design with four replicates and split plots was used. There was a significant interaction between the training system and rootstock for yield, number of clusters and foliar mass. The lyre system increased yield, cluster number and Ravaz index, favoring the development of more balanced grapevines. The IAC 572 rootstock promoted greater vigor by reducing yield, cluster number, bud fertility and Ravaz index. The other rootstocks were similar to each other in most variables. Net photosynthesis, stomatal conductance and instantaneous efficiency of water use were not influenced by the training system and the rootstock. The results obtained evidenced the influence of the training system associated to the rootstock on agronomic variable and yield of ‘Syrah’, recommending lyre training and grafting on 1103 Paulsen or IAC 313 in the semi-arid tropical conditions of the Vale do São Francisco.
Investigation of production efficiency and socio-economic factors of organic rice in Sumber Ngepoh district, Indonesia

Recently, environmental preservation and the back-to-nature approach to living have become a great lifestyle. The conditions for making organic rice have received a significant amount of attention in the rice market. The study of production efficiency will become substantial to the improvement of organic rice farming to fulfill rice demand. This study investigates the relevant variables which affect the production efficiency of organic rice. The Sumber Ngepoh is one of the largest districts in the rice-producing province of Indonesia. The production stochastic frontier function and the cost stochastic dual frontier is utilized to analyze the data. The technical, economic and allocative efficiency is analyzed to determine the significant variables. Moreover, the socio-economic variables are also investigated. The averages of the technical, allocative and economic efficiencies are 54.3%, 52%, and 31.3%, respectively, which are categorized as inefficient production. The averages indicate that organic rice farming in the Sumber Ngepoh District is not optimal and needs to be optimized. The results show that land, seed, organic fertilizer, organic pesticide, and hand tractor variables have a significant effect on organic rice production. The socio-economic variables which significantly affect all efficiency levels are farm size, experience, and family member.
Reproductive biology of the snake Liophis anomalus (Günther, 1858, Dipsadidae, Xenodontinae)

Correspondence: Alejandra Panzera (apanzera@fcien.edu.uy) We describe the reproductive pattern of Liophis anomalus based on examination of museum specimens from its entire distribution area. This species shows seasonal activity, although follicles in secondary vitellogenesis were found throughout the year. Our data suggest that multiple clutches occur within a single reproductive period. As in many other snakes, adult females are larger than males when sexual maturity is reached. The sexual size dimorphism index is 0.16, which is consistent with the absence of combat between males (a common feature among species belonging to the Xenodontini tribe). Testicular volume was positively correlated with male size. Clutch size averaged 7.37 eggs, was inversely correlated with mean egg size and positively correlated with female body size. Our results confirm that both phylogeny and climate influence reproductive patterns of this Xenodontini snake.
A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks

Complex molecular biological systems can be described in principle by reaction networks that explicitly take into account the sophisticated network of chemical interactions regulating cell life. Unfortunately, the effective utilization of such descriptions is often hindered by a pervasive problem: despite the wealth of qualitative graphical knowledge about network interactions, the form of the governing nonlinearities and/or the values of kinetic constants are hard to uncover experimentally. They can also change with environmental variations. Thus, it is desirable to have a theoretical framework to robustly guarantee the behavior of such networks, based only on graphical knowledge and applying regardless of the particular form of kinetics. This paper introduces a class of networks that are “structurally (mono) attractive” by which we mean that they are incapable of exhibiting multiple steady states, oscillation, or chaos by the virtue of their reaction graphs. These networks are characterized by the existence of a universal energy-like function which we call a Robust Lyapunov function (RLF). To find such functions, a finite set of rank-one linear systems is introduced, which form the extremals of a linear convex cone. The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a computational package, Lyapunov-Enabled Analysis of Reaction Networks (LEARN), is provided that constructs such functions or rules out their existence. An extensive study of biochemical networks demonstrates that LEARN offers a new unified framework. We study basic motifs, three-body binding, and transcriptional networks. We focus on cellular signalling networks including various post-translational modification cascades, phosphotransfer and phosphorelay networks, T-cell kinetic proofreading, and ERK signaling. We also study the Ribosome Flow Model. Arguably, the present approach identifies the largest class yet of biologically-relevant “attractive” networks. Author summary A theoretical and computational framework is developed for the identification of biochemical networks that are “structurally attractive”. This means they only allow global point attractors and they cannot exhibit any behavior such as multi-stability, oscillations, or chaos for any choice of the kinetics. They are characterized by the existence of energy-like functions. A computational package is made available for usage by a wider community. Many relevant networks in molecular biology satisfy the assumptions, and some are analyzed for the first time.
Shortest Path Routing on the Hypercube with Faulty Nodes

Interconnection networks are widely used in parallel computers. There are many topologies for interconnection networks and the hypercube is one of the most popular networks. There are a variety of different routing paradigms that need to be investigated on the hypercube. In this thesis we investigate the shortest path routing between two nodes on the hypercube when some nodes are faulty and cannot be used. In this thesis the shortest path between two nodes is considered as the Hamming distance of them. Regarding the shortest path problem in a faulty hypercube, some efficient algorithms have been proposed when each processor (node) has limited information regarding the status of other processors (whether they are faulty or not). There are also some proposed algorithms for the case where there is no limitation on the data of each processor but they are not efficient and are exponential in terms of number of faulty nodes and dimension of the hypercube. To check whether there is a shortest path between two given nodes in a faulty hypercube, we propose a polynomial algorithm with time complexity of O(nm) where n is the dimension of the hypercube and m is the number of faulty nodes. Our algorithm only requires the source node to know the state of all other nodes. The proposed algorithm first checks whether there is a shortest path from the source node to the target node and then it can construct it efficiently. Our idea is based on a so-called ordering and permutation model of paths in the hypercube. We use a constructive approach to find the path which is a permutation as well. We then use inclusion-exclusion and dynamic programming techniques to make our method efficient. We also propose an algorithm for counting all possible shortest paths in the hypercube.
Diet of bromeliad-frog Phyllodytes luteolus (Anura, Hylidae) in Atlantic Forest environments: what have the frogs been eating outside sandy coastal plains?

Knowledge about the diet of anurans in different environments is essential to understanding important aspects of their trophic ecology. The bromeliad-frog Phyllodytes luteolus inhabits tank bromeliads in sandy coastal plains and lowland forests on the mainland, as well as a continental island in southeastern Brazil. In this work, we describe and analyze the diet of P. luteolus in three environments. We obtained the consumed prey items of 92 frogs (32 from sandy coastal plain, 32 from lowland forest and 28 from the island) via a stomach-flushing procedure. We found some variations in consumed prey composition and prey volume across populations, but ants represented the most important consumed prey in all environments. Only ants had a relative importance greater than 50%, which may suggest a specialized diet that transcends the sandy coastal plain environment.
Psychoactive substances and sexually transmitted infections among military police officers from central-western, Brazil

The aim of this work was to evaluate the profile of military police officers regarding the use of psychoactive substances and the presence of Sexually Transmitted Infections (STI). Cross-sectional study carried out with military police officers in 2015 in the central-western, Brazil. The ASSIST (Alcohol, Smoking and Substance Involvement Screening Test) questionnaire was applied to investigate the use of psychoactive substances and serology was performed for syphilis, viral B and C hepatitis and HIV. Cronbach's alpha and Pearson Correlation Coefficient were employed. The ASSIST presented alpha coefficients of Cronbach almost perfect for tobacco (α=0.83) and substantial for the use of alcohol (α=0.70). Of 657 police officers, 78.5% consumed psychoactive substances at some point in their lives, with 76.7% alcohol, 28.5% tobacco, and 5.2% illegal psychoactive substances. A short intervention was required for 23.3% of police officers who used psychoactive substances, and 1.4% should be referred for treatment. Tobacco use was strongly associated with the use of more than one psychoactive substances in life (φ=0.9327), and the use of marijuana showed a moderate correlation with cocaine/crack (φ=0.5241). The prevalence of STI was 14.0%, being 7.6% for HBV, 6.8% syphilis, 0.5% HIV, and 0.3% HCV. HBV/syphilis and HBV/HIV co-infection were observed in 1.1% and 0.1%, respectively. There was no correlation between STI and use of psychoactive substances. The prevalence of HBV and syphilis was higher among police officers than in the general population. The ASSIST questionnaire was consistent when applied to this group and can be a significant tool for monitoring and decision making for timely intervention.