Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecology and evolution of acute infectiious diseases : the case of influenza

Cette these s'interesse aux interactions entre immunologie, epidemiologie et biologie evolutive. Nous utilisons une combinaison d'approches mathematiques et statistiques pour comprendre les processus gouvernant les dynamiques epidemiologiques et les phylogenies observees pour differents pathogenes de l'echelle individuelle aux populations. Nous prenons l'exemple de la grippe humaine. Trois hypotheses permettent de rendre compte de la phylodynamique particuliere de la grippe: (i) il existe un mecanisme de densite-dependance directe medie par une periode temporaire d'immunite totale apres infection ; (ii) le nombre de phenotypes possibles est limite, les virus les re-explorant sans cesse ; (iii) l'evolution de l'antigene principal de la grippe est ponctuee, les echappements ponctuels a l'immunite induisant des balayages selectifs. (iii) domine aujourd'hui et rend compte de la variabilite des epidemies de grippe, de larges echappements a l'immunite en induisant de plus grandes. Nous montrons que le formalisme ayant mene a (iii) induit de maniere implicite un processus immunologique irrealiste pour la grippe. Nous revelons que les series temporelles d'incidences grippales ne peuvent pas fournir une preuve du caractere ponctue de l'evolution antigenique, un modele parcimonieux prenant en compte une evolution antigenique purement graduelle les reproduisant. La nature chaotique de ces dynamiques marque une limite fondamentale a la predictibilite de la taille des epidemies de grippe et ce, independamment de la contingence evolutive. Nous developpons un formalisme confrontable aux donnees pour tester les differentes hypotheses rendant compte de la phylodynamique de la grippe.
Endothelial H2O2: a bad guy turning good?

About a decade ago everyone who read, at least occasionally, the science part of the local newspapers or followed popular science broadcasts “knew” that reactive oxygen species (ROS) are dangerous. They were thought to be bad, really bad, and many looking for a healthier lifestyle took action against these nasty small molecules accused of harming lipids and proteins by taking antioxidants like vitamin E. Food industry teamed up with pharmaceutical companies and brought up functional food enriched or supplemented with trustful antioxidants in the fight against ROS, which seemed to be produced under pathological conditions with just one mission: to damage the body. Things have changed during recent years, and there is emerging evidence that ROS are not only continuously produced even in healthy individuals but also exert important physiological functions. While we are still in-between a period that provides exciting new findings on the physiology of ROS, one can already summarize our present knowledge rather accurately by citing Paracelsus’ adage of “ Dosis (sola) facit venenum ” ( tertio defensio , 1538). See accompanying article on page 1774 The present work of Edwards et al1 is one of these exciting new reports that open our eyes to recognize the good side of the previously dammed ROS. This article deals with the effect of hydrogen peroxide (H2O2) on endothelium-derived hyperpolarization and is quite remarkable in several ways: First, the article is focused on EDHF (formerly termed endothelium-derived hyperpolarizing factor), a nitric oxide (NO) and prostacyclin-independent phenomenon of endothelium-dependent relaxation, of which the molecular mechanism and nature are still somewhat mysterious. Thus, this endothelium-dependent smooth muscle hyperpolarization has been attributed to either the formation and release of diffusible factors from the endothelium2 such as potassium ions (K+),3 cytochrome P450-derived arachidonic acid metabolites (epoxyeicosatrienoic acids), …
Impact of the prostatic apex on continence and urinary flow in patients with intestinal neobladders.

OBJECTIVE To determine the impact of preserving the prostatic apex on continence and urinary flow in patients with post-cystectomy intestinal bladder substitutes. PATIENTS AND METHODS A total of 38 male patients underwent radical cystectomy for bladder carcinoma and construction of a neobladder from ileum [9], sigmoid [9] or an ileocaecal segment [20]. The intestinal reservoir was anastomosed to the membranous urethra in 25 patients and to the apical prostatic capsule in 13. A subjective evaluation of urinary continence, uroflowmetry and urethral pressure profilometry were performed 1-3 years after surgery. RESULTS The only variable which showed a significant difference between patients with and without preservation of the prostatic apex was the functional profile length (P < 0.05). Conversely, there was no statistically significant difference in the continence result, peak flow rate and maximum urethral pressure between these two groups. However, there was a significant difference (P < 0.05) in peak flow rate among the three versions of neobladder in patients with a preserved prostatic apex (9.4 mL/s in ileal vs 15.8 mL/s in sigmoid and ileocaecal segments). CONCLUSION Preservation of the prostatic apex does not improve urinary continence in patients with intestinal neobladders and may present an element obstructing the evacuation of ileal bladders.
Relationship of visual dependence to age, balance, attention, and vertigo

[Purpose] The aim of this study was to investigate the relationship of increased visual dependence to age, balance, attention, and vertigo. [Subjects and Methods] Twelve younger, 12 visually independent (VI) older and 12 visually dependent (VD) older adults were assessed for levels of visual dependence using Subjective Visual Vertical (SVV) tilt values, balance ability using the Clinical Test of Sensory Integration for Balance (CTSIB), and attentional requirements through the dual-task paradigm and experience of vertigo by completing the Situational Vertigo Questionnaire (SVQ). [Results] VD older adults had higher SVV tilt values, greater postural sway in a scenario where visual and proprioceptive inputs were simultaneously altered, similar dual-task cost and lower SVQ scores compared with younger and VI older adults. No difference was observed between the latter two. [Conclusion] Visual dependence may not necessarily increase with age but affect balance in a sensory condition involving visual-proprioceptive conflict. There is a non-significant trend for elevated visual dependence with increased attentional demands. Greater visual dependence is not accompanied by more frequent symptoms of vertigo in visually complex environments.
Factors associated with the duration of breastfeeding amongst women in Perth, Australia

Duration of breastfeeding was studied in 556 women delivering at 2 maternity hospitals in Perth, Australia. At discharge 83.8% of women were breastfeeding their infants, including 6% who were giving complementary feeds. At 3 and 6 months, 61.8% and 49.9%, respectively, were still breastfeeding. In a Cox survival analysis of factors associated with duration of breastfeeding a positive association was found with maternal education, age and intended duration of breastfeeding. Male infants were more likely to be weaned before female infants and women whose partners were unemployed, or did not have a preference for breastfeeding, breastfed for shorter duration. There is still a need for programmes which support and encourage breastfeeding, focusing particularly on younger, less well‐educated women who intend to breastfeed for less than the recommended 4–6 months.
Many Fingers on the Mitotic Trigger: Post-Translational Regulation of the Cdc25C Phosphatase

AbstractThe mitotic inducer Cdc25 phosphatase controls the activation of Cdc2/cyclin B protein kinase and entry into mitosis in eukaryotic cells. Cdc25C is highly regulated by multiple post-translational modifications within its N-terminal regulatory domain and site-specific protein interactions. Phosphorylation of one inhibitory site targeted by multiple kinases determines the timing of Cdc25C activation and arrests cells in G2 in response to checkpoint, stress, developmental and extracellular signals. In mitosis, phosphorylation of several Ser/Thr residues and Pin1-catalysed peptidyl-proline isomerisation produces activation. Phosphorylation of one activating site is antagonistic to the proximal inhibitory site and maintains Cdc25C activity during mitosis. Phosphorylation and interacting proteins also modulate the nuclear import and export signals on Cdc25C, inducing dramatic changes in its localisation within the cell. Thus, the regulation of Cdc25C activity and localisation integrates multiple signals that govern the decision to enter mitosis.
Validity of Causal Inferences from Passive Longitudinal Analyses of Corrective Interventions : Accounting for Selection and Regression Artifacts

Analyses of passive longitudinal data can yield causally relevant evidence only to the extent that plausible alternative explanations are ruled out. This study compared the ability of five types of longitudinal analyses to correct for selection biases confounded with corrective interventions, using a cohort of 1464 4and 5-year-olds from Canadian NLSCY data. Three lines of evidence indicated that apparent child outcomes of corrective interventions were due to selection biases and accompanying regression artifacts. First, all significant effects of corrective interventions indicated apparently detrimental effects when predicting residualized change scores, but apparently beneficial effects when predicting simple change scores. This was true whether analyzing measured or latent variables. Second, results from temporally reversed analyses were consistent with selection and regression artifacts, not with unidirectional causal effects. Third, the findings were similar for empirically supported interventions (e.g., Ritalin, psychotherapy) and for parental interventions considered controversial (spanking, yelling). Typical longitudinal data may suppress the ability to detect causal effects due to lengthy inter-wave intervals and temporal overlap of covariates and causes. When applicable, longitudinal analyses should check for similar artifacts by implementing temporally reversed analyses and by determining whether the substantive results replicate without artifacts biased in their favor.
Functional Anatomy of Incisal Biting in Aplodontia rufa and Sciuromorph Rodents – Part 2: Sciuromorphy Is Efficacious for Production of Force at the Incisors

The protrogomorph condition of the rodent masticatory apparatus is thought to be present in only one living species, the mountain beaver Aplodontia rufa. The major anatomical difference between protrogomorphs and sciuromorphs is that the relative size of one part of the masseter muscle, the anterior lateral masseter, is much greater in sciuromorphs than in protrogomorphs. The mechanics of force production at the incisors were compared in A. rufa and six sciuromorph rodents. Is the sciuroid masticatory apparatus more effective for production of forces at the incisors during biting than the primitive, protrogomorph condition? To answer this question, three measures of mechanical ability were employed and three hypotheses were tested: (1) the mechanical advantage of the adductor musculature is greater in sciuromorphs than in A. rufa; (2) the relative force produced at the incisors is greater in sciuromorphs than in A. rufa, and (3) the relative amount of force produced that can be used to drive the incisors into an object, is greater in sciuromorphs than in A. rufa. The results demonstrated that the protrogomorph, A. rufa, is not as efficient at generating bite forces at the incisors as the sciuromorphs.
Maximum Likelihood Estimation in Dynamical Models of HIV

Summary The study of dynamical models of HIV infection, based on a system of nonlinear ordinary differential equations (ODE), has considerably improved the knowledge of its pathogenesis. While the first models used simplified ODE systems and analyzed each patient separately, recent works dealt with inference in non‐simplified models borrowing strength from the whole sample. The complexity of these models leads to great difficulties for inference and only the Bayesian approach has been attempted by now. We propose a full likelihood inference, adapting a Newton‐like algorithm for these particular models. We consider a relatively complex ODE model for HIV infection and a model for the observations including the issue of detection limits. We apply this approach to the analysis of a clinical trial of antiretroviral therapy (ALBI ANRS 070) and we show that the whole algorithm works well in a simulation study.
Simple method for correcting total protein in plasma for actual fibrinogen content.

Using plasma instead of serum for routine chemistry analyses has many advantages. To overcome the disadvantage of inclusively measuring fibrinogen in the plasma total protein assay without changing the clinical significance of the total protein assay, we investigated the possibility of subtracting the actual amount of fibrinogen from the plasma total protein. The correlation between serum and plasma total protein was excellent (plasma total protein = 0.989 x serum total protein + 6.7 g/L; r = 0.969; n = 131; mean difference = 5.55 g/L; P < 0.001). When the plasma total protein was corrected for the actual amount of fibrinogen, the correlation with serum total protein was equally good but the intercept was practically eliminated (corrected plasma total protein = 1.009 x serum total protein + 0.25 g/L; r = 0.985; n = 131; mean difference = 0.78 g/L; P = 0.47). The mean concentration of fibrinogen was 2.5 g/L (range: 1.38-3.62 g/L; n = 404) for blood donors, 3.6 g/L (n = 2707) for patients from the outpatient department, 4.6 g/L (n = 2023) for patients admitted to the hospital, and 6.6 g/L (n = 219) for patients whose concentration of C-reactive protein was > 50 mg/L. We conclude that the plasma total protein result should be corrected for the actual amount of fibrinogen.
At-speed delay testing of synchronous sequential circuits

Methods to test sequential circuits for delay faults are discussed. A method called at-speed testing is proposed for simplifying test application and reducing test length. A value system to allow at-speed testing is developed, and a test generation procedure is presented. The effect of at-speed test application on the path delay fault model is described. Experimental results are presented, demonstrating the applicability of at-speed testing and its effect on test length. <<ETX>>
Molecular Detection of Ancylostoma duodenale, Ancylostoma ceylanicum, and Necator americanus in Humans in Northeastern and Southern Thailand

The 2 principal species of hookworms infecting humans are Necator americanus and Ancylostoma duodenale. Case studies on zoonotic hookworm infections with Ancylostoma ceylanicum and/or Ancylostoma caninum are known mainly from Asian countries. Of these 2 zoonotic species, only A. ceylanicum can develop to adulthood in humans. In the present study, we report a molecular-based survey of human hookworm infections present in southern and northeastern Thailand. Thirty larval hookworm samples were obtained from fecal agar plate cultures of 10 patients in northeastren Thailand and 20 in southern Thailand. Partial ITS1, 5.8S, and ITS2 regions of the ribosomal DNA genes were amplified using PCR. The amplicons were sequenced, aligned, and compared with other hookworm sequences in GenBank database. The results showed that, in Thailand, N. americanus is more prevalent than Ancylostoma spp. and is found in both study areas. Sporadic cases of A. ceylanicum and A. duodenale infection were seen in northeastern Thailand.
The microscopical structure of the hippocampus in the rat.

The aim of this work was to study the rat's hippocampal formation by applying the light microscopic methods. The histological methods used to explore this region of the rat's brain were the Nissl technique, the Bielschowsky block impregnation method and the rapid Golgi technique. In the Nissl preparations, we identified only three fields of the hippocampus proprius (CA1, CA3 and CA4). CA2 was distinguished in the Bielschowsky impregnated blocks. The rapid Golgi technique, according the available literature, gives the best results by using the fresh samples. In this study, we reached good results by using formalin fixed sections. The layers of the hippocampal formation were differentiated. The pyramidal and granular cells were identified together with their axons and dendrites (Fig. 9, Ref. 22). Full Text (Free, PDF) www.bmj. sk.
Assessment of collagen fibril spacing in relation to selected region of interest (ROI) on electron micrographs—application to the mammalian corneal stroma

AIMS: To evaluate measurements of collagen fibril spacing using different shaped regions of interest (ROI) on transmission electron micrograph (TEM) images of rabbit corneal stroma. METHODS: Following glutaraldehyde fixation and phosphotungstic acid staining, TEM images of collagen fibrils in cross section were projected at a final magnification close to 250,000 × to obtain overlays. Interfibril distances (IFDs; center‐to‐center spacing) were measured within different ROIs of the same nominal area (0.25 μm2) but different shape (with the length to width, L:W, ratio from 1:1 to 6:1). The IFD distribution was analyzed, and the 2D organization assessed using a radial distribution analysis. RESULTS: The fibrils had an average diameter of 35.3 ± 3.8 (SD) nm, packing density of 393 ± 4 fibrils / μm2 and a fibril volume fraction of 0.39 ± 0.02. IFDs ranged from 29 to 1400 nm depending on the shape of the ROI, with average values ranging from 263 to 443 nm. By artificially selecting IFD data only to a radial distance of 250 nm, the average IFDs were just 145–157 nm. The radial distributions, to 250 nm, all showed a nearest neighbors first peak which shifted slightly from predominantly at 45–54 nm with more rectangular ROIs. The radial distribution profiles could be shown to be statistically different if the ROI L:W ratio was 2:1 or greater. CONCLUSION: Selection of an ROI for assessment of packing density and interfibril distances should be standardized for comparative assessments of TEMs of collagen fibrils. Microsc. Res. Tech., 2011. © 2011 Wiley‐Liss, Inc.
Development of a combined radiation and full thickness burn injury minipig model to study the effects of uncultured adipose-derived regenerative cell therapy in wound healing

Abstract Purpose: To develop an approach that models the cutaneous healing that occurs in a patient with full thickness thermal burn injury complicated by total body radiation exposure sufficient to induce sub-lethal prodromal symptoms. An assessment of the effects of an autologous cell therapy on wound healing on thermal burn injury with concomitant radiation exposure was used to validate the utility of the model. Methods: Göttingen minipigs were subjected to a 1.2 Gy total body irradiation by exposure to a 6 MV X-ray linear accelerator followed by ∼10 cm2 full thickness burns (pre-heated brass block with calibrated spring). Three days after injury, wounds were excised to the underlying fascia and each animal was randomized to receive treatment with autologous adipose-derived regenerative cells (ADRC) delivered by local or intravenous injection, or vehicle control. Blood counts were used to assess radiation-induced marrow suppression. All animals were followed using digital imaging to assess wound healing. Full-thickness biopsies were obtained at 7, 14, 21 and 30 days’ post-treatment. Results: Compared to animals receiving burn injury alone, significant transient neutropenia and thrombocytopenia were observed in irradiated subjects with average neutrophil nadir of 0.79 × 103/μl (day 15) and platelet nadir of 60 × 103/μl (day 12). Wound closure through a combination of contraction and epithelialization from the wound edges occurred over a period of approximately 28 days’ post excision and treatment. Re-epithelialization was accelerated in wounds treated with ADRC (mean 3.5-fold increase at 2 weeks post-treatment relative to control). This acceleration was accompanied by an average 67% increase in blood vessel density and 30% increase in matrix (collagen) deposition. Similar results were observed when ADRC were injected either directly into the wound or by intravenous administration. Conclusions: Although preliminary, this study provides a reproducible minipig model of thermal burn injury complicated by myelosuppressive total body irradiation that utilizes standardized procedures to evaluate novel countermeasures for potential use following attack by an improvised nuclear device.
Medicaid as an Investment in Children: What is the Long-Term Impact on Tax Receipts?

We examine the long-term impact of expansions to Medicaid and the State Children's Health Insurance Program that occurred in the 1980's and 1990's. With administrative data from the IRS, we calculate longitudinal health insurance eligibility from birth to age 18 for children in cohorts affected by these expansions, and we observe their longitudinal outcomes as adults. Using a simulated instrument that relies on variation in eligibility by cohort and state, we find that children whose eligibility increased paid more in cumulative taxes by age 28. These children collected less in EITC payments, and the women had higher cumulative wages by age 28. Incorporating additional data from the Medicaid Statistical Information System (MSIS), we find that the government spent $872 in 2011 dollars for each additional year of Medicaid eligibility induced by the expansions. Putting this together with the estimated increase in tax payments discounted at a 3% rate, assuming that tax impacts are persistent in percentage terms, the government will recoup 56 cents of each dollar spent on childhood Medicaid by the time these children reach age 60. This return on investment does not take into account other benefits that accrue directly to the children, including estimated decreases in mortality and increases in college attendance. Moreover, using the MSIS data, we find that each additional year of Medicaid eligibility from birth to age 18 results in approximately 0.58 additional years of Medicaid receipt. Therefore, if we scale our results by the ratio of beneficiaries to eligibles, then all of our results are almost twice as large.