Miracle-dz/UniFAR-FTUs huggingface dataset:
Residue analysis of organochlorine pesticides in water and sediments from Agboyi Creek, Lagos

Microlayer water, mixed layer water, epipellic and benthic sediments were collected from Agboyi Creek, Lagos to analyse organochlorine pesticide residues. Sampling was conducted between December 2008 and September 2009 during the dry and wet seasons to study effects of seasonal variation on the samples. Water samples were subjected to liquid-liquid extraction using dichloromethane, while sediments were subjected to cold extraction with petroleum ether/acetone (1:1 v/v) mixture and clean-up on silica gel adsorbents. The samples were analyzed for aldrin, dieldrin, endrin, DDT, heptachlor, HCH, endosulfan, chlordane and methoxychlor. The detection and determination of the pesticide residues were performed by injecting 1 µL of purified extract into the injection port of a gas chromatograph with a 63Ni electron capture detector (GC-µECD Agilent 7890A) equipped with ChemStation software. Pesticide residues in the epipellic and benthic sediments were higher than the residues in the water. The mixed layer water showed enhanced levels of residues when compared with the microlayer water. The residue levels were higher during the dry season than the wet season. The levels of residues in the water and sediments were below the maximum permissive residue limits. Key words: Agboyi Creek, organochlorine pesticides, microlayer water, mixed layer water, epipellic sediment, benthic sediment
Calcium-mediated actin reset (CaAR) mediates acute cell adaptations

Actin has well established functions in cellular morphogenesis. However, it is not well understood how the various actin assemblies in a cell are kept in a dynamic equilibrium, in particular when cells have to respond to acute signals. Here, we characterize a rapid and transient actin reset in response to increased intracellular calcium levels. Within seconds of calcium influx, the formin INF2 stimulates filament polymerization at the endoplasmic reticulum (ER), while cortical actin is disassembled. The reaction is then reversed within a few minutes. This Calcium-mediated actin reset (CaAR) occurs in a wide range of mammalian cell types and in response to many physiological cues. CaAR leads to transient immobilization of organelles, drives reorganization of actin during cell cortex repair, cell spreading and wound healing, and induces long-lasting changes in gene expression. Our findings suggest that CaAR acts as fundamental facilitator of cellular adaptations in response to acute signals and stress. DOI: http://dx.doi. org/10.7554/eLife.19850. 001
Corneal Thickness Profile Changes After Femtosecond LASIK for Hyperopia

Purpose: To compare changes in the corneal thickness profile before and 6 months after femtosecond laser in situ keratomileusis (LASIK) for hyperopia. Methods: In a prospective noncomparative case series study, 24 eyes of 20 hyperopic patients undergoing femtosecond LASIK were examined preoperatively and 6 months postoperatively. Corneal profile was measured using Pentacam HR device. Paired t test was used to compare preoperative and postoperative values. Spearman correlation analysis was performed to evaluate the relationship between the central corneal thickness changes and attempted spherical equivalent refraction (SER). Results: The mean uncorrected distance visual acuity significantly improved after surgery (P<0.001). Significant differences in central, midperipheral, ablative annular, and peripheral corneal thicknesses were observed from preoperatively to 6 months postoperatively (all P<0.001). There was no significant correlation between the changes in the central corneal thickness and attempted SER (P=0.23). Conclusions: The corneal thicknesses across the whole ablation zone including central corneal thickness, significantly decrease postoperatively compared with preoperatively.
MicroRNA‐31 targets FIH‐1 to positively regulate corneal epithelial glycogen metabolism

Corneal epithelium relies on abundant glycogen stores as its primary energy source. MicroRNA‐31 (miR‐31), a corneal epithelial‐preferred miRNA, negatively regulates factor inhibiting hypoxia‐inducible factor‐1 (FIH‐1). Since HIF‐1α is involved in anaerobic energy production, we investigated the role that miR‐31 and FIH‐1 play in regulating corneal epithelial glycogen. We used antagomirs (antago) to reduce the level of miR‐31 in primary human corneal epithelial keratinocytes (HCEKs), and a miR‐31‐resistant FIH‐1 to increase FIH‐1 levels. Antago‐31 raised FIH‐1 levels and significantly reduced glycogen stores in HCEKs compared to irrelevant‐antago treatment. Similarly, HCEKs retrovirally transduced with a miR‐31‐resistant FIH‐1 had markedly reduced glycogen levels compared with empty vector controls. In addition, we observed no change in a HIF‐1α reporter or known genes downstream of HIF‐1α indicating that the action of FIH‐1 and miR‐31 on glycogen is HIF‐1α‐independent. An enzyme‐dead FIH‐1 mutation failed to restore glycogen stores, indicating that FIH‐1 negatively regulates glycogen in a hydroxylase‐independent manner. FIH‐1 overexpression in HCEKs decreased AKT signaling, activated GSK‐3β, and inactivated glycogen synthase. Treatment of FIH‐1‐transduced HCEKs with either a myristolated Akt or a GSK‐3β inhibitor restored glycogen stores, confirming the direct involvement of Akt/GSK‐3β signaling. Silencing FIH‐1 in HCEKs reversed the observed changes in Akt‐signaling. Glycogen regulation in a HIF‐1α‐independent manner is a novel function for FIH‐1 and provides new insight into how the corneal epithelium regulates its energy requirements. —Peng, H. , Hamanaka, R. B. , Katsnelson, J., Hao, L. , Yang, W. , Chandel, N. S. , Lavker, R. M. MicroRNA‐31 targets FIH‐1 to positively regulate corneal epithelial glycogen metabolism. FASEB J. 26, 3140–3147 (2012). www.fasebj. org
Neural Oscillation Reveals Deficits in Visuospatial Working Memory in Children With Developmental Coordination Disorder.

The electroencephalographic (EEG) oscillations associated with visuospatial working memory (VSWM) were examined in children with developmental coordination disorder (DCD; 10-11 years; N = 29) and typically developing (TD) children (10-11 years; N = 29). Behaviorally, DCD showed poorer VSWM than TD, which coincided with the diminished ability of DCD in modulating neural oscillations. Furthermore, prestimulus oscillatory alpha activity was correlated with VSWM performance. The results suggest that children with DCD might have a reduced ability to encode and recognize new information, and in particular have difficulty in maintaining task-relevant information, resulting in poorer VSWM. This study thus concludes that changes in oscillatory EEG activity reflect some of the problems leading to cognitive deficits in DCD.
Characteristics of Physicians Who Dismiss Families for Refusing Vaccines

BACKGROUND AND OBJECTIVES: Physicians dismissing families who refuse vaccines from their practices is controversial. We assessed the following among pediatricians (Peds) and family physicians (FPs): (1) reported prevalence of parental refusal of 1 or more vaccines in the infant series; (2) physician response to refusal; and (3) the association between often/always dismissing families and provider/practice characteristics and state exemption laws. METHODS: Nationally representative survey conducted June to October 2012. A multivariable analysis assessed association of often/always dismissing families with physician/practice characteristics, state philosophical exemption policy, and degree of difficulty obtaining nonmedical exemptions. RESULTS: The response rate was 66% (534/815). Overall, 83% of physicians reported that in a typical month, ≥1% of parents refused 1 or more infant vaccines, and 20% reported that >5% of parents refused. Fifty-one percent reported always/often requiring parents to sign a form if they refused (Peds 64%, FP 29%, P < .0001); 21% of Peds and 4% of FPs reported always/often dismissing families if they refused ≥1 vaccine. Peds only were further analyzed because few FPs dismissed families. Peds who dismissed families were more likely to be in private practice (adjusted odds ratio [aOR] 4.90, 95% confidence interval [CI] 1.40–17.19), from the South (aOR 4.07, 95% CI 1.08–15.31), and reside in a state without a philosophical exemption law (aOR 3.70, 95% CI 1.74–7.85). CONCLUSIONS: Almost all physicians encounter parents who refuse infant vaccines. One-fifth of Peds report dismissing families who refuse, but there is substantial variation in this practice. Given the frequency of dismissal, the impact of this practice on vaccine refusers and on pediatric practices should be studied.
Pneumococcal bacteremia. Review of 111 cases, 1957--1969, with special reference to cases with undetermined focus.

The clinical significance of pneumococcal bacteremia was evaluated from the hospital records of 111 infants and children. Focal infections other than nasopharyngitis were recognized in 96 patients (86%). Pneumonia and otitis were equally frequent, together accounting for 71% of the infections. More than one focus was recognized in 30 patients (27%). In 30 patients, no focus of pneumococcal infection was detected before the positive result of the blood culture was reported; a focus was subsequently found in 15 of them. In 11 patients "upper-respiratory tract infections," and in 4 patients fever provided the only clinical evidence of infection. There were four deaths among the 111 patients: one in a newborn, one with terminal leukemia, and two with meningitis.
Bipolar or unipolar hemiarthroplasty after femoral neck fracture in the geriatric population.

BACKGROUND The choice of prosthesis in hemiarthroplasty is controversial for geriatric patients after femoral neck fracture. We hypothesised that selection criteria for unipolar or bipolar prostheses could be constructed based on factors affecting mortality. AIMS THE AIMS OF THIS RETROSPECTIVE STUDY WERE: (1) to determine the factors affecting mortality of femoral neck fracture patients ≥65 years of age; (2) to compare patient mortality rates, radiological findings, and functional outcomes according to prosthesis type (unipolar or bipolar); and (3) to evaluate the persistence of inner bearing mobility of bipolar prostheses. STUDY DESIGN Retrospective comparative study. METHODS In total, 144 patients operated for hemiarthroplasty and aged ≥65 were included. We classified the patients into either unipolar or bipolar prosthesis groups. To reveal factors that affected mortality, age, sex, delay in surgery, and American Society of Anesthesiologists score were obtained from folders. Barthel Daily Living, Harris hip, and acetabular erosion scores were calculated and bipolar head movement was analysed for live patients. RESULTS One-year mortality was 31.94%. Age ≥75 (p=0.029), male sex (p=0.048), and delay in surgery ≥6 (p=0.004) were the patient characteristics that were related to increased mortality. There were no significant differences in sex, age, American Society of Anesthesiologists score, delay in surgery, mortality, or Barthel, Harris, acetabulum scores between the two groups. Twenty patients from each group were admitted for last follow-up. Bipolar head movement was preserved for 33.3% of patients. They were inactive patients with low Barthel and Harris scores. CONCLUSION Although bipolar head movement was preserved in inactive patients, we suppose that this conferred no advantage to these patients, who could hardly walk. In this study, male patients, those aged ≥75 years, and those operated at ≥6 days had an increased risk of mortality. Also, although not significant in multivariate analysis, high American Society of Anesthesiologists score (≥3) was related to increased mortality. Considering that one of three patients died during the first postoperative year, we think that these patients should be operated as soon as possible, and expensive bipolar prostheses must be used selectively in regard to patient characteristics.
Analyse génomique de la coinfection par le virus VIH et VHC

Plus de 170 millions d'individus sont infectes par le VHC dans le monde et 37 millions par le VIH. La coinfection VIH/VHC est frequente et represente un element cle de la prise en charge des patients infectes par le VIH. Depuis l'arrivee des HAART, les maladies du foie sont devenues la cause principale de mortalite chez les patients coinfectes VIH/VHC. L'evolution naturelle et le pronostic de l'hepatite C sont plus severes en cas de coinfection par le VIH du fait d'une fibrose acceleree et d'une evolution rapide vers la cirrhose et ses complications. Certains facteurs accelerant la fibrose hepatique sont clairs aujourd'hui comme: l'absence de recours au traitement anti-VHC, la replication active du VHC et la consommation excessive d'alcool. De plus, il existe de plus en plus de preuves que les variants genetiques contribuent a la fibrose hepatique chez les patients monoinfectes par le VHC, mais cet aspect a ete peu etudie dans la coinfection VIH/VHC.Durant ma these, j'ai eu acces aux donnees d'un echantillon de 494 patients coinfectes genotypes issu de la cohorte ANRS CO13 HEPAVIH. L'histoire naturelle du VIH et du VHC y est renseignee de maniere tres detaillee et le suivi clinique des patients permet d'avoir des informations precises sur l'etat de fibrose hepatique. J'ai pu alors realiser deux etudes d'association « genome-entier » pour identifier des polymorphismes associes a la severite de la fibrose a l'aide de donnees completes de 292 patients. La premiere etude a mis en evidence une association entre la quantification de l'elasticite hepatique par Fibroscan® et un locus, egalement replique dans la monoinfection par le VHC. Cette association a permis d'identifier deux genes impliques dans des mecanismes de maintien de structure et de signalisation cellulaire (CAV3) mais aussi dans la replication du VHC (RAD18). La seconde etude a identifie deux associations significatives en comparant deux groupes de scores METAVIR (F0F1F2 vs F3F4), en particulier dans le gene CTNND2 qui est implique dans un reseau d'interaction associe a des mecanismes moleculaires lie a des maladies hepatiques.Ces deux etudes sont en cours de publication dans des revues scientifiques internationales a comite de lecture. Ces nouvelles perspectives dans la comprehension des mecanismes de fibrose dans le contexte de la coinfection VIH/VHC pourraient aider a l'identification de nouvelles cibles pour la creation de medicaments ou de tests diagnostiques afin d'ameliorer les soins des patients.
Neural networks: Efficient implementations and applications

This paper serves as an overview to the special session “Neural Networks: Efficient Implementations and Applications” on IEEE International Conference on ASIC (ASICON) 2017. Focusing on the state-of-the-art research progresses on neural networks, our introduction consists of two main parts, namely efficient hardware implementations and the latest applications. Deep neural network (DNN) provides superior performance for complex tasks, which pushes one step further in many fields. However, in the development of DNN, a lot of challenges emerge and remain to be settled. In this overview paper, latest research progress of neural network in both implementation and application will be summarized to open the discussion on some important to-be-solved problems and limitations, especially from the circuits-and-systems design perspective. This motivates the organization of this special session, which includes this overview paper and four technical papers. An outline of these four invited papers constructs the last part of this overview, sketching their targeted research problems, proposed methodologies and solutions, as well as the main contribution and results.
Impaired Pulmonary Arterial Vasoconstriction and Nitric Oxide–Mediated Relaxation Underlie Severe Pulmonary Hypertension in the Sugen-Hypoxia Rat Model

Pulmonary vasoreactivity could determine the responsiveness to vasodilators and, in turn, the prognosis of pulmonary hypertension (PH). We hypothesized that pulmonary vasoreactivity is impaired, and we examined the underlying mechanisms in the Sugen-hypoxia rat model of severe PH. Male Sprague-Dawley rats were injected with Sugen (20 mg/kg s.c.) and exposed to hypoxia (9% O2) for 3 weeks, followed by 4 weeks in normoxia (Su/Hx), or treated with Sugen alone (Su) or hypoxia alone (Hx) or neither (Nx). After hemodynamic measurements, the heart was assessed for right ventricular hypertrophy (Fulton’s index); the pulmonary artery, aorta, and mesenteric arteries were isolated for vascular function studies; and contractile markers were measured in pulmonary arteries using quantitative polymerase chain reaction (PCR). Other rats were used for morphometric analysis of pulmonary vascular remodeling. Right ventricular systolic pressure and Fulton’s index were higher in Su/Hx versus Su, Hx, and Nx rats. Pulmonary vascular remodeling was more prominent in Su/Hx versus Nx rats. In pulmonary artery rings, contraction to high KCl (96 mM) was less in Su/Hx versus Nx and Su, and phenylephrine-induced contraction was reduced in Su/Hx versus Nx, Hx, and Su. Acetylcholine (ACh)-induced relaxation was less in Su/Hx versus Nx and Hx, suggesting reduced endothelium-dependent vasodilation. ACh relaxation was inhibited by nitric oxide synthase (NOS) and guanylate cyclase blockade in all groups, suggesting a role of the NO-cGMP pathway. Nitrate/nitrite production in response to ACh was less in Su/Hx versus Nx, supporting reduced endothelial NO production. Sodium nitroprusside (10−8 M) caused less relaxation in Su/Hx versus Nx, Hx, and Su, suggesting a decreased responsiveness of vascular smooth muscle (VSM) to vasodilators. Neither contraction nor relaxation differed in the aorta or mesenteric arteries of all groups. PCR analysis showed decreased expression of contractile markers in pulmonary artery of Su/Hx versus Nx. The reduced responsiveness to vasoconstrictors and NO-mediated vasodilation in the pulmonary, but not systemic, vessels may be an underlying mechanism of severe PH in Su/Hx rats and appears to involve attenuation of the NO relaxation pathway and a switch of pulmonary VSM cells to a synthetic less reactive phenotype.
Confocal laser scanning microscopy: using cuticular autofluorescence for high resolution morphological imaging in small crustaceans

The utility of cuticular autofluorescence for the visualization of copepod morphology by means of confocal laser scanning microscopy (CLSM) was examined. Resulting maximum intensity projections give very accurate information on morphology and show even diminutive structures such as small setae in detail. Furthermore, CLSM enables recognition of internal structures and differences in material composition. Optical sections in all layers and along all axes of the specimens can be obtained by CLSM. The facile and rapid preparation method bears no risk of artefacts or damage occurring to the preparations and the visualized specimens can be used for later analyses allowing for the investigation of irreplaceable type specimens or parts of them. These features make CLSM a very effective tool for both taxonomical and ecological studies in small crustaceans; however, the maximum thickness of the specimens is limited to a few hundred micrometers. Three‐dimensional models based on CLSM image stacks allow observation of the preparations from all angles and can permit, improve and speed up studies on functional morphology. The visualization method described has a strong potential to become a future standard technique in aquatic biology due to its advantages over conventional light microscopy and scanning electron microscopy.
Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase

Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target. ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) helicase is a superfamily 1 helicase containing seven conserved motifs. We have cloned, expressed, and purified a Strep-fused recombinant MERS-CoV nonstructural protein 13 (M-nsp13) helicase. Characterization of its biochemical properties showed that it unwound DNA and RNA similarly to severe acute respiratory syndrome CoV nsp13 (S-nsp13) helicase. We showed that M-nsp13 unwound in a 5′-to-3′ direction and efficiently unwound the partially duplex RNA substrates with a long loading strand relative to those of the RNA substrates with a short or no loading strand. Moreover, the Km of ATP for M-nsp13 is inversely proportional to the length of the 5′ loading strand of the partially duplex RNA substrates. Finally, we also showed that the rate of unwinding (ku) of M-nsp13 is directly proportional to the length of the 5′ loading strand of the partially duplex RNA substrate. These results provide insights that enhance our understanding of the biochemical properties of M-nsp13. IMPORTANCE Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target.
Dietary Transition in the South Asian Diaspora: Implications for Diabetes Prevention Strategies.

BACKGROUND South Asians (SA) have a four to five fold higher risk for type 2 diabetes mellitus (T2DM) in comparison to other Asian migrant groups. Dietary patterns have been attributed as an important independent modifiable risk factor. OBJECTIVE The aim of this review is to document the dietary patterns of SA migrants in Western countries and to summarize the evidence for the association of dietary patterns with T2DM and its predisposing factors. METHODS Using key search words articles from 1990 onwards were sourced from MEDLINE Pro- Quest and PubMed (not MEDLINE) databases for this narrative review. RESULTS A significant shift in meal pattern with frequent dining out and eating fast foods, traditional festival foods and Western desserts and snacks was common among SA. Consumption of potatoes, dairy, oil, meat and fish increased and beans, lentils, fruits and vegetables decreased post-migration. "Animal protein" and "fried snacks, sweets and high-fat dairy" were associated with greater insulin resistance and lower HDL cholesterol. A "mixed" dietary pattern was associated with obesity and hypertension and a "western" dietary pattern was associated with overall risk for Metabolic Syndrome. A 70% increase in the odds of diabetes per standard deviation in gram of protein intake was also observed. CONCLUSION Dietary patterns pave the way to develop diabetes and other obesity related diseases among SA as duration of residence increases. The first five years since migration maybe a window of opportunity to provide targeted interventions to ensure maintenance of healthy dietary habits.