Miracle-dz/UniFAR-FTUs huggingface dataset:
Farm-Level Risk Factors for Fish-Borne Zoonotic Trematode Infection in Integrated Small-Scale Fish Farms in Northern Vietnam

Background Northern Vietnam is an endemic region for fish-borne zoonotic trematodes (FZT), including liver and intestinal flukes. Humans acquire the FZT infection by eating raw or inadequately cooked fish. The production of FZT-free fish in aquaculture is a key component in establishing a sustainable program to prevent and control the FZT transmission to humans. Interventions in aquaculture should be based on knowledge of the main risk factors associated with FZT transmission. Methodology/Principal Findings A longitudinal study was carried out from June 2006 to May 2007 in Nam Dinh province, Red River Delta to investigate the development and risk factors of FZT infections in freshwater cultured fish. A total of 3820 fish were sampled six times at two-month intervals from 96 fish farms. Logistic analysis with repeated measurements was used to evaluate potential risk factors based on information collected through questionnaire interviews with 61 fish farm owners. The results showed that the FZT infections significantly increased from first sampling in June to July 2006 (65%) to sixth sampling in April to May, 2007 (76%). The liver fluke, Clonorchis sinensis and different zoonotic intestinal flukes including Haplochis pumilio, H. taichui, H. yokogawai, Centrocestus formosanus and Procerovum varium were found in sampled fish. Duration of fish cultured (sampling times), mebendazole drug self-medication of household members, presence of snails in the pond, and feeding fish with green vegetation collected outside fish farms all had a significant effect on the development of FZT prevalence in the fish. Conclusions/Significance The FZT prevalence in fish increased by 11 percentage points during a one-year culture period and the risk factors for the development of infection were identified. Results also highlight that the young fish are already highly infected when stocked into the grow-out systems. This knowledge should be incorporated into control programs of FZT transmission in integrated small-scale aquaculture nursery and grow-out systems in Vietnam.
Minimally invasive plate osteosynthesis: Applications and techniques in dogs and cats

Summary Bone plating has been used as a method of fracture management for many years. Recently, a trend toward the use of fracture fixation techniques which preserve the local fracture environment, known as biological osteosynthesis, has evolved. This trend has resulted in the development of a less traumatic method of bone plating referred to as minimally invasive plate osteosynthesis (MIPO), or percutaneous plating. During MIPO fracture stabilisation, plates are inserted through short incisions and a communicating epiperiosteal tunnel. Typically, bone plates applied in this fashion have a bridging function. Promising outcomes have been reported in human patients undergoing MIPO fracture stabilisation, and limited reports of the use of this technique in dogs and cats have yielded positive results as well. Careful case selection, pre-operative planning, and appropriate instrumentation are necessary when performing the technique. Rapid time to union, low complication rates and good return to function have been noted in human patients. Additional research is needed to define selection criteria and outline the definitive benefits of MIPO in dogs and cats.
A framework for the adaptive ﬁnite element solution of large inverse problems. I. Basic techniques

Since problems involving the estimation of distributed coeﬃcients in partial diﬀerential equations are numerically very challenging, eﬃcient methods are indispensable. In this ﬁrst part of a series, we will introduce a framework for the eﬃcient solution of such problems. This comprises the use of adaptive ﬁnite element schemes, eﬃcient solvers for the large linear systems arising from discretization, and methods to treat additional information in the form of inequality constraints on the parameter sought. The methods to be developed will be based on an all-at-once approach, in which the inverse problem is solved through a Lagrangian formulation. In order to allow for discretizations that are adaptively reﬁned as nonlinear iterations proceed, all algorithms are formulated in a continuous function-space setting. Numerical examples will demonstrate the applicability of the method for problems with several million unknowns and more than 10,000 parameters. This article also deﬁnes the notation and basic methods used in subsequent parts to develop a posteriori error estimates, upon which optimal discretizations will be based.
Lateral Supraorbital Approach vs Pterional Approach: An Anatomic Qualitative and Quantitative Evaluation

BACKGROUND: Several minimally invasive modifications of the standard pterional approach have been proposed recently. The lateral supraorbital approach is one of these modifications. OBJECTIVE: To provide a qualitative and quantitative anatomic comparison of the surgical exposure and the operability afforded by the standard pterional approach and the lateral supraorbital approach. METHODS: Eight pterional approaches and 8 lateral supraorbital approaches were used in 8 fresh human cadaver heads. One qualitative and 2 quantitative tools were used to assess the surgical exposure. RESULTS: Qualitatively, the lateral supraorbital approach has the advantages of reduced trauma to the temporalis muscle and exposure that is comparable to that provided by the standard pterional approach to the sellar and suprasellar regions. This approach offers limited exposure of the interpeduncular fossa compared with the pterional one. Quantitatively, the pterional approach provides a greater surgical volume than the lateral supraorbital approach (32.90 mL vs 23.60 mL with P < .05). Also, the pterional approach provides a greater associated surgical operability than the lateral supraorbital approach (exposure score of 66 and 53, respectively). However, the lateral supraorbital approach offers an equivalent access to the anterior communicating artery complex, optic nerve, optic chiasm, and sellar area (the exposure scores were 19 for both approaches). CONCLUSION: From an anatomic point of view, both approaches provide similar exposure to the sellar, suprasellar, and anterior communicating artery areas. The pterional approach provides better exposure of the retrosellar area. The ability to operate in the retrosellar area, as judged by our model, was higher with the pterional than with the lateral supraorbital approach.
Autistic Children Show a Surprising Relationship between Global Visual Perception, Non-Verbal Intelligence and Visual Parvocellular Function, Not Seen in Typically Developing Children

Despite much current research into the visual processing style of individuals with Autism Spectrum Disorder (ASD), understanding of the neural mechanisms is lagging, especially with respect to the contributions of the overlapping dichotomies of magnocellular/parvocellular (afferent neural pathways), global/local (perception) and dorsal/ventral (cortical streams). Here, we addressed this deficiency by measuring inspection times (ITs) for novel global/local stimuli as well as recording nonlinear visually evoked potentials (VEPs), in particular, magnocellular and parvocellular temporal efficiencies. The study was conducted on a group of male ASD children and a typically developing (TD) group matched for mean age and mean non-verbal intelligence, as measured by the Raven’s Progressive Matrices. The IT results did not differ between groups, however a negative correlation between global IT and Raven’s score was found in the ASD group, that was not evident in the TD group. Nonlinear VEP showed the ASD group had smaller amplitude parvocellular-generated second order responses compared to the TD group. This is a sign of improved temporal responsiveness in ASD vs. TD groups. Principal Component Analysis linked global IT, non-verbal intelligence scores and VEP parvocellular efficiency in a single factor for the ASD but not the TD group. The results are suggestive of a constraint on pathways available for cognitive response in the ASD group, with temporal processing for those with ASD becoming more reliant on the parvocellular pathway.
Cu/Zn-superoxide dismutase and glutathione peroxidase during aging.

During oxidative metabolism harmful reactive oxygen species (ROS) are generated. These species are neutralized by antioxidant enzymes. Firstly, superoxide dismutase (Sod) converts superoxide radicals (.O2-) to hydrogen peroxide (H2O2). Thereafter catalase (Cat) and glutathione peroxidase (Gpx) independently convert this to water. An imbalance in the ratio of Sod to Gpx and Cat results in the accumulation of H2O2 which may participate in the Fenton reaction, resulting in the formation of noxious hydroxyl radicals. These ROS are highly reactive and cause damage to macromolecules such as DNA, protein and lipids. We propose that it is the balance in the activity of the Sod to Gpx plus Cat ratio (Sod/(Gpx plus Cat)) that is an important determinant of cellular aging. This is based on our observation that an altered Cu/Zn-superoxide dismutase (Sod1)/(Gpx1 plus Cat) ratio exists in the brain of aging mice and that this correlates with increased lipid damage. Conversely, aging liver and kidney have an unaffected Sod1/(Gpx1 plus Cat) ratio and lipid damage is not increased with aging. We also examine the Sod1 to Gpx1 ratio in Down syndrome tissue and show that all organs have an altered ratio. This may contribute to the premature aging seen in these individuals. We show that binding of a p50/p65 complex to an NF-kappa B consensus sequence is enhanced by H2O2 treatment in NIH3T3 cells. Thus an altered Sod1/(Gpx1 plus Cat) ratio may also affect gene expression by altering the binding and/or availability of transcription factors to DNA.
VNR Algorithm: A Greedy Approach for Virtual Networks Reconfigurations

In this paper we address the problem of virtual network reconfiguration. In our previous work on virtual network embedding strategies, we found that most virtual network rejections were caused by bottlenecked substrate links while peak resource use is equal to 18%. These observations lead us to propose a new greedy Virtual Network Reconfiguration algorithm, VNR. The main aim of our proposal is to 'tidy up' substrate network in order to minimise the number of overloaded substrate links, while also reducing the cost of reconfiguration. We compare our proposal with the related reconfiguration strategy VNA-Periodic, both of them are incorporated in the best existing embedding strategies VNE-AC and VNE-Greedy in terms of rejection rate. The results obtained show that VNR outperforms VNA-Periodic. Indeed, our research shows that the performances of VNR do not depend on the virtual network embedding strategy. Moreover, VNR minimises the rejection rate of virtual network requests by at least 83% while the cost of reconfiguration is lower than with VNA-Periodic.
Toxin Profile of Gymnodinium catenatum (Dinophyceae) from the Portuguese Coast, as Determined by Liquid Chromatography Tandem Mass Spectrometry

The marine dinoflagellate Gymnodinium catenatum has been associated with paralytic shellfish poisoning (PSP) outbreaks in Portuguese waters for many years. PSP syndrome is caused by consumption of seafood contaminated with paralytic shellfish toxins (PSTs), a suite of potent neurotoxins. Gymnodinium catenatum was frequently reported along the Portuguese coast throughout the late 1980s and early 1990s, but was absent between 1995 and 2005. Since this time, G. catenatum blooms have been recurrent, causing contamination of fishery resources along the Atlantic coast of Portugal. The aim of this study was to evaluate the toxin profile of G. catenatum isolated from the Portuguese coast before and after the 10-year hiatus to determine changes and potential impacts for the region. Hydrophilic interaction liquid chromatography tandem mass spectrometry (HILIC-MS/MS) was utilized to determine the presence of any known and emerging PSTs in sample extracts. Several PST derivatives were identified, including the N-sulfocarbamoyl analogues (C1–4), gonyautoxin 5 (GTX5), gonyautoxin 6 (GTX6), and decarbamoyl derivatives, decarbamoyl saxitoxin (dcSTX), decarbamoyl neosaxitoxin (dcNeo) and decarbamoyl gonyautoxin 3 (dcGTX3). In addition, three known hydroxy benzoate derivatives, G. catenatum toxin 1 (GC1), GC2 and GC3, were confirmed in cultured and wild strains of G. catenatum. Moreover, two presumed N-hydroxylated analogues of GC2 and GC3, designated GC5 and GC6, are reported. This work contributes to our understanding of the toxigenicity of G. catenatum in the coastal waters of Portugal and provides valuable information on emerging PST classes that may be relevant for routine monitoring programs tasked with the prevention and control of marine toxins in fish and shellfish.
Non-linear gravitational clustering: smooth halos, substructures and scaling exponents

Within the framework of hierarchical clustering scenarios, we investigate the consequences for the properties of virialized halos of the constraints provided by numerical simulations on the first few correlation functions. Thus, we show that the density field cannot be described by a collection of smooth halos with a universal density profile. This implies that substructures within larger objects play an important role (but a mean spherically averaged density profile may exist). In particular, a possible interpretation is that collapsed objects can be divided into an infinite hierarchy of smaller objects with increasingly large densities (these substructures might also be continuously destroyed and created by the long-range action of gravity). Finally, we present multifractal models (restricted to non-linear scales) which can describe in a natural way such non-linear density fields with increasingly large fluctuations at smaller scales. We relate their properties to the correlation functions and present a few constraints they are expected to satisfy, using theoretical considerations as well as constraints from numerical simulations. Thus, the simplest realistic model is the bifractal model described in Balian & Schaeffer (1989a). Moreover, we show that it should provide (at least) a very good approximation of the multifractal properties of the actual non-linear density field, hence of the probability distribution of the density contrast. The implications of this model (e.g. for galaxies) are detailed in other studies.
Update on the pathological processes, molecular biology, and clinical utility of N-acetylcysteine in chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a common and morbid disease characterized by high oxidative stress. Its pathogenesis is complex, and involves excessive oxidative stress (redox imbalance), protease/antiprotease imbalance, inflammation, apoptosis, and autoimmunity. Among these, oxidative stress has a pivotal role in the pathogenesis of COPD by initiating and mediating various redox-sensitive signal transduction pathways and gene expression. The protective physiological mechanisms of the redox balance in the human body, their role in the pathogenesis of COPD, and the clinical correlation between oxidative stress and COPD are reviewed in this paper. N-acetylcysteine (NAC) is a mucolytic agent with both antioxidant and anti-inflammatory properties. This paper also reviews the use of NAC in patients with COPD, especially the dose-dependent properties of NAC, eg, its effects on lung function and the exacerbation rate in patients with the disease. Earlier data from BRONCUS (the Bronchitis Randomized on NAC Cost-Utility Study) did not suggest that NAC was beneficial in patients with COPD, only indicating that it reduced exacerbation in an “inhaled steroid-naïve” subgroup. With regard to the dose-dependent properties of NAC, two recent randomized controlled Chinese trials suggested that high-dose NAC (1,200 mg daily) can reduce exacerbations in patients with COPD, especially in those with an earlier (moderately severe) stage of disease, and also in those who are at high risk of exacerbations. However, there was no significant effect on symptoms or quality of life in patients receiving NAC. Further studies are warranted to investigate the effect of NAC at higher doses in non-Chinese patients with COPD.
An Auxin Transport-Based Model of Root Branching in Arabidopsis thaliana

Root architecture is a crucial part of plant adaptation to soil heterogeneity and is mainly controlled by root branching. The process of root system development can be divided into two successive steps: lateral root initiation and lateral root development/emergence which are controlled by different fluxes of the plant hormone auxin. While shoot architecture appears to be highly regular, following rules such as the phyllotactic spiral, root architecture appears more chaotic. We used stochastic modeling to extract hidden rules regulating root branching in Arabidopsis thaliana. These rules were used to build an integrative mechanistic model of root ramification based on auxin. This model was experimentally tested using plants with modified rhythm of lateral root initiation or mutants perturbed in auxin transport. Our analysis revealed that lateral root initiation and lateral root development/emergence are interacting with each other to create a global balance between the respective ratio of initiation and emergence. A mechanistic model based on auxin fluxes successfully predicted this property and the phenotype alteration of auxin transport mutants or plants with modified rythms of lateral root initiation. This suggests that root branching is controlled by mechanisms of lateral inhibition due to a competition between initiation and development/emergence for auxin.
The Aspergillus fumigatus pkcA G579R Mutant Is Defective in the Activation of the Cell Wall Integrity Pathway but Is Dispensable for Virulence in a Neutropenic Mouse Infection Model

Aspergillus fumigatus is an opportunistic human pathogen, which causes the life-threatening disease, invasive pulmonary aspergillosis. In fungi, cell wall homeostasis is controlled by the conserved Cell Wall Integrity (CWI) pathway. In A. fumigatus this signaling cascade is partially characterized, but the mechanisms by which it is activated are not fully elucidated. In this study we investigated the role of protein kinase C (PkcA) in this signaling cascade. Our results suggest that pkcA is an essential gene and is activated in response to cell wall stress. Subsequently, we constructed and analyzed a non-essential A. fumigatus pkcA G579R mutant, carrying a Gly579Arg substitution in the PkcA C1B regulatory domain. The pkcA G579R mutation has a reduced activation of the downstream Mitogen-Activated Protein Kinase, MpkA, resulting in the altered expression of genes encoding cell wall-related proteins, markers of endoplasmic reticulum stress and the unfolded protein response. Furthermore, PkcAG579R is involved in the formation of proper conidial architecture and protection to oxidative damage. The pkcA G579R mutant elicits increased production of TNF-α and phagocytosis but it has no impact on virulence in a murine model of invasive pulmonary aspergillosis. These results highlight the importance of PkcA to the CWI pathway but also indicated that additional regulatory circuits may be involved in the biosynthesis and/or reinforcement of the A. fumigatus cell wall during infection.
Establishment of a Protein Reference Map for Soybean Root Hair Cells1[W][OA]

Root hairs are single tubular cells formed from the differentiation of epidermal cells on roots. They are involved in water and nutrient uptake and represent the infection site on leguminous roots by rhizobia, soil bacteria that establish a nitrogen-fixing symbiosis. Root hairs develop by polar cell expansion or tip growth, a unique mode of plant growth shared only with pollen tubes. A more complete characterization of root hair cell biology will lead to a better understanding of tip growth, the rhizobial infection process, and also lead to improvements in plant water and nutrient uptake. We analyzed the proteome of isolated soybean (Glycine max) root hair cells using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and shotgun proteomics (1D-PAGE-liquid chromatography and multidimensional protein identification technology) approaches. Soybean was selected for this study due to its agronomic importance and its root size. The resulting soybean root hair proteome reference map identified 1,492 different proteins. 2D-PAGE followed by mass spectrometry identified 527 proteins from total cell contents. A complementary shotgun analysis identified 1,134 total proteins, including 443 proteins that were specific to the microsomal fraction. Only 169 proteins were identified by the 2D-PAGE and shotgun methods, which highlights the advantage of using both methods. The proteins identified are involved not only in basic cell metabolism but also in functions more specific to the single root hair cell, including water and nutrient uptake, vesicle trafficking, and hormone and secondary metabolism. The data presented provide useful insight into the metabolic activities of a single, differentiated plant cell type.
Outcome of one-stage treatment of developmental dysplasia of hip in older children

Background The principles of treatment of congenital dislocation of hip in old children are different than those of infants and neonates. The purpose of this study is to evaluate the radiographic and functional results of one-stage treatment (open reduction, femoral shortening derotation, and Salter’s osteotomy) of DDH in older children. Materials and Methods Between January 2005 and June 2010, 25 patients (30 hips) underwent one-stage triple procedure of open reduction, femoral shortening derotation, and Salter’s osteotomy for the treatment of DDH. Preoperatively, they were classified according to the Tönnis class. Clinical outcomes were assessed using the modified McKay’s criteria to measure pain symptoms, gait pattern, Trendelenburg sign status, and the range of hip joint movement. Radiographic assessment was made using Severin’s scoring method to measure the centre-edge angle and dysplasia. Results The mean age at the time of operation was 3.9 years (range 1.6–8 years), and the average duration of followup was 4.1 years (range 2–7.6 years). The McKay’s score was excellent in 13 hips, good in 14 hips, fair in 2, and poor in 1 hip. The Severin’s class I and II was found in 25 (83.3%) hips at the time of final evaluation as compared to none at the time of presentation. Conclusions Young children having DDH can safely be treated with an extensive one-stage triple procedure of open reduction, femoral shortening derotation, and Salter’s osteotomy, without increasing the risk of AVN. Early diagnosis and intervention is the successful treatment of patients suffering from DDH.
Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

The recent observation of pseudocontact shifts (pcs) in 13C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., 13C-,15N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and 13C-,15N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.