Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the salinity adaptation mechanism in Penicilliopsis clavariiformis AP, a rare salt tolerant fungus from mangrove

Penicilliopsis clavariiformis AP, a rare salt tolerant fungus reported for the first time from India was identified through polyphasic taxonomy. Scanning electron microscopy showed that the fungus has unique features such as biverticillate penicilli bearing masses of oval to ellipsoidal conidia. The fungus has been characterized for salt tolerance and to understand the relevance of central carbon metabolism in salt stress adaptation. It showed optimal growth at 24 °C and able to tolerate up to 10% (w/v) NaCl. To understand the mechanism of adaptation to high salinity, activities of the key enzymes regulating glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle were investigated under normal (0% NaCl) and saline stress environment (10% NaCl). The results revealed a re‐routing of carbon metabolism away from glycolysis to the pentose phosphate pathway (PPP), served as a cellular stress‐resistance mechanism in fungi under saline environment. The detection and significant expression of fungus genes (Hsp98, Hsp60, HTB, and RHO) under saline stress suggest that these halotolerance conferring genes from the fungus could have a role in fungus protection and adaptation under saline environment. Overall, the present findings indicate that the rearrangement of the metabolic fluxes distribution and stress related genes play an important role in cell survival and adaptation under saline environment.
Augmented Berlin-Frankfurt-Munster therapy abrogates the adverse prognostic significance of slow early response to induction chemotherapy for children and adolescents with acute lymphoblastic leukemia and unfavorable presenting features: a report from the Children's Cancer Group.

PURPOSE Compared with previous Children's Cancer Group (CCG) acute lymphoblastic leukemia (ALL) trials, therapy based on the Berlin-Frankfurt-Munster (BFM) 76 trial has effected an improvement in event-free survival (EFS). In an attempt to improve EFS further, CCG investigators formulated an augmented BFM (A-BFM) regimen that provides prolonged, intensified postinduction chemotherapy relative to the CCG-modified BFM regimen. PATIENTS AND METHODS We tested A-BFM in 101 patients with ALL and unfavorable presenting features that showed slow early response (SER) to induction therapy who attained remission on day 28. Their outcome was compared with that of 251 concurrent patients with unfavorable presenting features, a rapid early response to therapy (RER), and remission by day 28, treated with CCG-BFM with or without cranial radiation (CRT). RESULTS The 4-year EFS rate from the end of induction for SER patients treated with A-BFM was 70.8% +/- 4.6%. Seventeen patients remain in continuous remission beyond 5 years. Vincristine (VCR) neurotoxicity developed in 50% of patients, but was rarely debilitating. Allergies to Escherichia coli L-asparaginase (L-ASP) occurred in 35% of patients. Avascular necrosis of bone (AVN) developed in 9% of patients. In comparison, a concurrent RER group treated with standard BFM +/- CRT had a 4-year EFS rate of 73.1% +/- 4.6%. CONCLUSION The toxicity of A-BFM is significant, but acceptable. Compared with historical control SER patients treated with CCG-modified BFM, A-BFM therapy appears to produce a significant improvement in EFS. This is the first study to show that intensive chemotherapy, as given in the A-BFM regimen, can abrogate the adverse prognostic significance of SER.
Noninvasive Demonstration of In Vivo 3‐Fluoro‐3‐Deoxy‐D‐Glucose Metabolism in Rat Brain by 19F Nuclear Magnetic Resonance Spectroscopy: Suitable Probe for Monitoring Cerebral Aldose Reductase Activities

The metabolism of 3‐fluoro‐3‐deoxy‐D‐glucose (3‐FDG) in rat brain in vivo was investigated noninvasively using 19F nuclear magnetic resonance (NMR) Spectroscopy. Following an intravenous infusion of 3‐FDG, 400 mg/kg, four resonances assigned to the α and β anomers of 3‐FDG, 3‐fluoro‐3‐deoxy‐D‐sorbitol, and 3‐fluoro‐3‐deoxy‐D‐fructose were clearly resolved in brain, a result indicating that 3‐FDG is metabolized primarily into the aldose reductase sorbitol (ARS) pathway. An orally administered aldose reductase inhibitor, sorbinil, caused reduction of the flux of 3‐FDG into the ARS, an observation suggesting that the method can be applied in quantitative studies of ARS path way activities. Studies of 24‐h urine specimens showed that in addition to the two metabolites observed in brain, F‐was excreted into the urine. 3‐FDG appears to be a suitable metabolic probe for assessing glucose metabolism in the ARS pathway by in vivo 19F NMR Spectroscopy.
A review of chemical therapies for treating diabetic hypertension

ABSTRACT Introduction: Hypertension and diabetes are two of the most important modifiable risk factors for cardiovascular and renal disease. The majority of patients with diabetes also have high blood pressure (BP) and the presence of hypertension in these patients dramatically increases cardiovascular and renal risk. Areas covered: This article will discuss chemical therapies for hypertension in patients with diabetes, based on currently available evidence on the effects of antihypertensive treatment on metabolic profile and renal endpoints that are the factors mostly influencing drug choice. Expert opinion: Several lines of evidence suggest that angiotensin-converting-enzyme-inhibitors (ACEIs), angiotensin-receptor-blockers (ARBs) and calcium-channel-blockers (CCBs) have beneficial or neutral effects on carbohydrate metabolism, whereas old β-blockers and thiazide diuretics have not. Renal outcome trials clearly suggest that in proteinuric diabetic CKD ACEIs and ARBs reduce the rate of disease progression. Thus, an ACEI or an ARB, if tolerated, should be the first choice in diabetic individuals, followed by CCBs, vasodilating β-blockers and diuretics, depending on the individual patient characteristics. Recent studies suggest that the novel antidiabetic class of sodium-glucose co-transporter 2 inhibitors may offer a small reduction in BP together with important decrease in incidence of cardiovascular and renal events in patients with type 2 diabetes.
A Scalable Checkpoint Encoding Algorithm for Diskless Checkpointing

Diskless checkpointing is an efficient technique to save the state of a long running application in a distributed environment without relying on stable storage. In this paper, we introduce several scalable encoding strategies into diskless checkpointing and reduce the overhead to survive k failures in p processes from 2[logp]. k((beta + 2gamma)m + alpha) to (1 + O(1/radic(m))). k(beta + 2gamma)m, where a is the communication latency, 1/beta is the network bandwidth between processes, 1/gamma is the rate to perform calculations, and m is the size of local checkpoint per process. The introduced algorithm is scalable in the sense that the overhead to survive k failures in p processes does not increase as the number of processes p increases. We evaluate the performance overhead of the introduced algorithm by using a preconditioned conjugate gradient equation solver as an example. Experimental results demonstrate that the introduced techniques are highly scalable.
Strand switching during rolling circle replication of plasmid-like DNA circles in the mitochondria of the higher plant Chenopodium album (L.).

The structure of sigma-like mitochondrial DNA molecules prepared from suspension cultured cells of Chenopodium album (L.) was studied by electron microscopy. These molecules were highly variable in size, ranging from about 1 to 104 kb, and had single- and double-stranded regions typical for rolling circle replicating intermediates. Partial denaturation studies confirmed that these structures constitute rolling circles. Close inspection of the circle-tail junctions of the replication fork at high magnification suggests that in circles with a double-stranded tail, both strands of the tail seem to be covalently attached to the circle in about 27% of the molecules. This observation can be explained by a phenomenon called strand switching or strand splippage during rolling circle replication, similar to a mechanism proposed for bacterial replicons or in vitro replicating constructs harboring bacteriophage T4 replication origins.
Prevalence and associated factors of minor neuromotor dysfunctions at age 5 years in prematurely born children: the EPIPAGE Study.

OBJECTIVES To assess the frequency of minor neuromotor dysfunctions (MNDs) at age 5 years according to gestational age, to test their association with behavioral and learning difficulties, and to find determining neonatal factors. DESIGN Prospective population-based cohort study of children born in 1997 and followed up from birth to age 5 years. SETTING All maternity wards in 9 regions of France. PARTICIPANTS A total of 1662 children born before 33 completed weeks of gestation and 2 control groups including 245 children born at 33 to 34 weeks and 332 children born at 39 to 40 weeks. Main Exposure Birth before 33 weeks. Main Outcome Measure Short version of the Touwen neurological examination classifying children as healthy, having mild MND (MND-1), or having moderate MND (MND-2) depending on the number of abnormal neuromotor signs found. RESULTS Of children born before 33 weeks, 41.4% had MND-1 and 3.0% had MND-2. These proportions were 30.8% and 0.5%, respectively, for children born at 33 to 34 weeks and 22.0% and 0.7%, respectively, for children born at 39 to 40 weeks. Minor neuromotor dysfunction was independently associated with learning difficulties at age 5 years (odds ratio [OR], 1.6; 95% confidence interval [CI], 1.1-2.2). In very preterm children, factors associated with MND-1 were postnatal corticotherapy (OR, 1.8; 95% CI, 1.3-2.6), multiple births (OR, 0.7; 95% CI, 0.6-0.9), and, in singletons, breastfeeding (OR, 0.8; 95% CI, 0.6-0.99). Being a boy (OR, 3.1; 95% CI, 1.5-6.4), having had acute fetal distress (OR, 2.8; 95% CI, 1.4-5.5) or severe abnormalities on early cranial ultrasonography (OR, 2.7; 95% CI, 1.2-6.2), and having had postnatal corticotherapy (OR, 2.7; 95% CI, 1.2-6.1) increased the risk of MND-2. CONCLUSIONS The high rate of MNDs and their association with an increased risk for learning difficulties justify their screening in case of (even moderate) prematurity.
In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors

ABSTRACT We attempted to select HIV-1 variants resistant to darunavir (DRV), which potently inhibits the enzymatic activity and dimerization of protease and has a high genetic barrier to HIV-1 development of resistance to DRV. We conducted selection using a mixture of 8 highly multi-protease inhibitor (PI)-resistant, DRV-susceptible clinical HIV-1 variants (HIV-1MIX) containing 9 to 14 PI resistance-associated amino acid substitutions in protease. HIV-1MIX became highly resistant to DRV, with a 50% effective concentration (EC50) ∼333-fold greater than that against HIV-1NL4-3. HIV-1MIX at passage 51 (HIV-1MIXP51) replicated well in the presence of 5 μM DRV and contained 14 mutations. HIV-1MIXP51 was highly resistant to amprenavir, indinavir, nelfinavir, ritonavir, lopinavir, and atazanavir and moderately resistant to saquinavir and tipranavir. HIV-1MIXP51 had a resemblance with HIV-1C of the HIV-1MIX population, and selection using HIV-1C was also performed; however, its DRV resistance acquisition was substantially delayed. The H219Q and I223V substitutions in Gag, lacking in HIV-1CP51, likely contributed to conferring a replication advantage on HIV-1MIXP51 by reducing intravirion cyclophilin A content. HIV-1MIXP51 apparently acquired the substitutions from another HIV-1 strain(s) of HIV-1MIX through possible homologous recombination. The present data suggest that the use of multiple drug-resistant HIV-1 isolates is of utility in selecting drug-resistant variants and that DRV would not easily permit HIV-1 to develop significant resistance; however, HIV-1 can develop high levels of DRV resistance when a variety of PI-resistant HIV-1 strains are generated, as seen in patients experiencing sequential PI failure, and ensuing homologous recombination takes place. HIV-1MIXP51 should be useful in elucidating the mechanisms of HIV-1 resistance to DRV and related agents.
The insulin-like growth factor pathway is altered in spinocerebellar ataxia type 1 and type 7

Polyglutamine diseases are inherited neurodegenerative disorders caused by expansion of CAG repeats encoding a glutamine tract in the disease-causing proteins. There are nine disorders, each having distinct features but also clinical and pathological similarities. In particular, spinocerebellar ataxia type 1 and 7 (SCA1 and SCA7) patients manifest cerebellar ataxia with degeneration of Purkinje cells. To determine whether the disorders share molecular pathogenic events, we studied two mouse models of SCA1 and SCA7 that express the glutamine-expanded protein from the respective endogenous loci. We found common transcriptional changes, with down-regulation of insulin-like growth factor binding protein 5 (Igfbp5) representing one of the most robust changes. Igfbp5 down-regulation occurred in granule neurons through a non-cell-autonomous mechanism and was concomitant with activation of the insulin-like growth factor (IGF) pathway and the type I IGF receptor on Purkinje cells. These data define one common pathogenic response in SCA1 and SCA7 and reveal the importance of intercellular mechanisms in their pathogenesis.
No observed effect of ocean acidification on nitrogen biogeochemistry in a summer Baltic Sea plankton community

Abstract. Nitrogen fixation by filamentous cyanobacteria supplies significant amounts of new nitrogen (N) to the Baltic Sea. This balances N loss processes such as denitrification and anammox, and forms an important N source supporting primary and secondary production in N-limited post-spring bloom plankton communities. Laboratory studies suggest that filamentous diazotrophic cyanobacteria growth and N2-fixation rates are sensitive to ocean acidification, with potential implications for new N supply to the Baltic Sea. In this study, our aim was to assess the effect of ocean acidification on diazotroph growth and activity as well as the contribution of diazotrophically fixed N to N supply in a natural plankton assemblage. We enclosed a natural plankton community in a summer season in the Baltic Sea near the entrance to the Gulf of Finland in six large-scale mesocosms (volume ∼ 55 m3) and manipulated fCO2 over a range relevant for projected ocean acidification by the end of this century (average treatment fCO2: 365–1231 µatm). The direct response of diazotroph growth and activity was followed in the mesocosms over a 47 day study period during N-limited growth in the summer plankton community. Diazotrophic filamentous cyanobacteria abundance throughout the study period and N2-fixation rates (determined only until day 21 due to subsequent use of contaminated commercial 15N-N2 gas stocks) remained low. Thus estimated new N inputs from diazotrophy were too low to relieve N limitation and stimulate a summer phytoplankton bloom. Instead, regeneration of organic N sources likely sustained growth in the plankton community. We could not detect significant CO2-related differences in neither inorganic nor organic N pool sizes, or particulate matter N : P stoichiometry. Additionally, no significant effect of elevated CO2 on diazotroph activity was observed. Therefore, ocean acidification had no observable impact on N cycling or biogeochemistry in this N-limited, post-spring bloom plankton assemblage in the Baltic Sea.
Shotgun mass mapping of Lactobacillus species and subspecies from caries related isolates by MALDI‐MS

A taxonomical study of 90 isolates of lactobacilli isolated from soft and hard carious dentine of 70 deciduous molars is presented. The Lactobacillus strains were determined by shotgun mass mapping (SMM). This method based on MALDI‐MS analysis of Lactobacillus isolates treated with trypsin followed by database comparison against a library of mass spectra derived from 20 reference strains. The SMM method allowed to discriminate different Lactobacillus subspecies. The method was used to analyse Lactobacillus isolates of unknown identity derived from carious dentine. Application of the SMM method to isolates from hard carious dentine revealed a nearly similar distribution of L. paracasei ss paracasei (29%), L. paracasei ss tolerans (32%) and L. casei ss rhamnosus (23%) as dominant subspecies. On the other hand, samples derived from soft carious dentine showed a clear bias only to L. paracasei ss paracasei (60%), whereas L. paracasei ss tolerans (14%) and L. casei ss rhamnosus (12%) were clear minorities. Compared to existent methods, SMM has unique potential for the analysis of Lactobacillus strains on subspecies level.
Implementing an edge-fog-cloud architecture for stream data management

The Internet of Moving Things (IoMT) requires support for a data life cycle process ranging from sorting, cleaning and monitoring data streams to more complex tasks such as querying, aggregation, and analytics. Current solutions for stream data management in IoMT have been focused on partial aspects of a data life cycle process, with special emphasis on sensor networks. This paper aims to address this problem by developing streaming data life cycle process that incorporates an edge/fog/cloud architecture that is needed for handling heterogeneous, streaming and geographically-dispersed IoMT devices. We propose a 3-tier architecture to support an instant intra-layer communication that establishes a stream data flow in real-time to respond to immediate data life cycle tasks in the system. Communication and process are thus the defining factors in the design of our stream data management solution for IoMT. We describe and evaluate our prototype implementation using real-time transit data feeds. Preliminary results are showing the advantages of running data life cycle tasks for reducing the volume of data streams that are redundant and should not be transported to the cloud.
Onset and evolution of stunting in infants and children. Examples from the Human Nutrition Collaborative Research Support Program. Kenya and Egypt studies.

The etiology of the early onset of stunting is diverse among populations of varying biological, environmental and cultural circumstances. This is exemplified within the Nutrition CRSP project, which took place in three different populations and ecological conditions. Within each study area a different mix and varying proportions of causative factors were identified. At least in Kenya, and probably in Mexico, the problem has its antecedents in prepregnancy and pregnancy. Powerful determinants of the infants' size at birth and during the first 6 months of life are maternal size upon entry into pregnancy, and weight and fat gain during pregnancy and lactation. In all three countries a low pregnancy weight gain was observed. Notably in Kenya, where the energy intake of the mother decreases progressively throughout pregnancy, not only do mothers gain only half as much as European or North American women, but they even lose weight and fat in the last month of pregnancy, and some mothers gain no weight or lose weight during the whole of pregnancy. Mothers in Kenya start lactation with relatively poor fat stores. Although their energy intake increases somewhat during lactation, preliminary estimates suggest that these increases may be insufficient to maintain their bodily integrity, to carry out their normal tasks of daily living, and to produce a sufficient amount of milk for optimal infant growth. In addition to an energy deficit, diet quality is a problem, particularly in Kenya and Mexico and less so in Egypt. Intakes of animal products and animal protein are very low. Zinc and iron intakes are not only low, but the bioavailability of these nutrients is poor because of the high phytate, fiber and tea content of the diet. Also vitamin B12 intake is extremely low, and at least mild-to-moderate iodine deficiency (IDD) is present in Kenya. The above micronutrients have been demonstrated to affect the linear growth of the Kenyan children, even after confounding factors have been controlled. The early use of supplemental feeding in Kenya is a double-edged sword. On the one hand, there is a slight increase in febrile illness and possible displacement of breast milk intake in the supplemented infants, although mothers do not decrease breast feeding frequency and duration. On the other hand, even the modest amounts of available zinc and B12 in supplemental foods appear to have a positive effect on linear growth. (ABSTRACT TRUNCATED AT 400 WORDS)
Validity of an On-Court Lactate Threshold Test in Young Basketball Players

Castagna, C, Manzi, V, Impellizzeri, F, Chaouachi, A, Ben Abdelkrim, N, and Ditroilo, M. Validity of an on-court lactate threshold test in young basketball players. J Strength Cond Res 24(9): 2434-2439, 2010-The aim of this study was to assess the criterion validity of a submaximal field test (Intermittent Shuttle-Running Test [ISRT]) for lactate threshold (LT) detection in young basketball players. Fourteen basketball players (age 15.3 ± 0.6 years, height 182 ± 4.6 cm, and body mass 71.6 ± 6.3 kg) were submitted in random order and on separate occasions, to ISRT (20-m shuttle running for 4 minutes at 9, 10 and 11 km·h−1) and to a treadmill intermittent progressive test (criterion validity, TM) devised for the assessment of LT (4-minute stages at 8, 10, 12, 14 km·h−1). Blood-lactate concentrations [La]b were assessed taking earlobe blood samples at rest and immediately after each of the 4-minute running steps considered for ISRT and TM. Lactate threshold was considered as the running speed attained at 1 mmol·L−1 [La]b above resting levels. Results showed that speed at LT during ISRT and TM was significantly related (r = 0.82, p < 0.001). However, speed at LT during the ISRT showed to be significantly lower than the speed at LT during TM (10.1 ± 1.7 vs. 12 ± 2.3 km·h−1, p < 0.001). During ISRT, players attained 80 ± 4.7, 87 ± 4.4, and 92 ± 3.0% of maximal heart rate (HR) at 9, 10, and 11 km·h−1, respectively. This study results show that ISRT may be used as a valid field test to assess submaximal aerobic fitness in young team-sport players. Continuous 20-m shuttle running performed at 11 km·h−1 revealed to elicit HR in the range of those reported to induce aerobic-fitness development in trained subjects. In light of study finding, ISRT may be considered in testing batteries for basketball players to complement anaerobic fitness and agility.
Deep Learning for Mortgage Risk

We examine the behavior of mortgage borrowers over several economic cycles using an unprecedented dataset of origination and monthly performance records for over 120 million mortgages originated across the United States between 1995 and 2014. Our deep learning model of multi-period mortgage delinquency, foreclosure, and prepayment risk uncovers the highly nonlinear influence on borrower behavior of an exceptionally broad range of loan-specific and macroeconomic variables down to the zip-code level. In particular, most variables strongly interact. Prepayments involve the greatest nonlinear effects among all events. We demonstrate the significant implications of the nonlinearities for risk management, investment management, and mortgage-backed securities.