Miracle-dz/UniFAR-FTUs huggingface dataset:
Outcomes of laparoscopic common bile duct exploration (LCBDE) after failed endoscopic retrograde cholangiopancreatography versus primary LCBDE for managing cholecystocholedocholithiasis

Objective This study was performed to compare the outcomes of laparoscopic common bile duct exploration (LCBDE) after failed endoscopic retrograde cholangiopancreatography (ERCP) versus primary LCBDE for managing cholecystocholedocholithiasis. Methods We retrospectively analyzed data from 59 patients who underwent LCBDE during laparoscopic cholecystectomy (LC) for managing cholecystocholedocholithiasis from January 2013 to August 2019. The patients underwent either primary LCBDE plus LC (Group I) or LCBDE plus LC after failed ERCP (Group II). The demographics, reason for ERCP failure, perioperative details, and postoperative outcomes were evaluated. Results CBD stone removal using preoperative ERCP failed in 31 patients (Group II) because of remaining stones after ERCP (n = 9), failed cannulation (n = 6), failed sedation (n = 6), a periampullary diverticulum (n = 5), previous Billroth II gastrectomy (n = 3), a huge stone (n = 1), and an impacted stone (n = 1). The CBD stone clearance rate was >96% in both groups. The mean operative time, hospital stay, overall complication rate, and open conversion rate were not significantly different between the two groups. Conclusions When extraction of CBD stones by ERCP is likely to be difficult or fail, primary LCBDE is an acceptable alternative treatment for managing cholecystocholedocholithiasis.
Filamentous organism bulking in nutrient removal activated sludge systems. Paper 6: Review, evaluation and consolidation of results

The finding that the selector effect did not control bulking by low food to micro-organism ratio (F/M) filaments, concluded this research direction that was considered to hold promise for controlling low F/M filament proliferation, and placed this research back into an exploratory phase. In this paper, the information collected so far in the research programme is evaluated together with that published in the literature, in order to delineate new research directions aimed at solving the low F/M filament bulking problem. In the conclusions, a framework is established that provided guidance for the subsequent research.
Effects of dietary soy sauce oil supplementation on growth performance and sensory characteristics of Biwa salmon Oncorhynchus masou rhodurus

Soy sauce oil (SSO) is a byproduct of soy sauce manufacturing. SSO is uncommon as an ingredient for fish or animal feeds. The present study evaluated the dietary effects of SSO on fish growth performance, fillet fat content, and sensory characteristics of the fillets. Biwa salmon Oncorhynchus masou rhodurus (initial mean body weight of 176 g) were fed in commercial aquaculture ponds with either the SSO-supplemented diet or the soybean oil (SBO)-supplemented diet (as a control) for 94 days. Dietary supplementation of SSO at 5% did not cause any adverse ef fects on fish performance, morphometric measurement, or sensory traits compared with the control fish. Dietary SSO supplementation resulted in significant improvements in some organoleptic properties of fish fillets, which were favored by certain groups of people. The present results indicate that dietary SSO can be used as an alternative ingredient replacing SBO in fish feeds. This is the first study to sensorially evaluate SSO-fed fish.
Modelling the effect of high, constant temperature on food intake in young growing pigs

Performance in pigs is greatly reduced during periods of heat stress through a reduction in voluntary food intake (VFI). However, little information is available as to what extent growth in piglets is affected by high temperature. The objective of this study was therefore to quantify the change in VFI as affected by environmental temperature. Piglets, initially 15·5 (s.e. 1·9) kg body weight (BW), were individually housed and exposed over a period of 17 days to either 19, 21, 23, 25, 27, 29, 31, 33, or 35oC. Animals had ad libitum access to a starter diet and water. VFI was measured daily whereas BW was determined twice weekly. Over the 17 days, daily VFI and BW gain were proportionately 0·48 and 0·51 lower at 35oC than at 19oC. Due to the reduced VFI at high temperatures, the average BW during the experiment was greater at low temperatures than at high temperatures. Consequently, part of the difference in VFI is directly due to temperature and part may be explained by cascading, indirect effects (i.e. the increased BW). To account for this, VFI was expressed as a power function of BW (VFI = aBW b ). It was assumed that environmental temperature affected the scalar (a) through a quadratic or a ‘plateau-linear decline’ function of temperature. The VFI appeared relatively constant between 19 and 25oC (0·096 (kg/day)/(kg BW0·83)) and decreased thereafter. Between 25 and 35oC, VFI decreased on average by proportionately 0·28 in a 20-kg pig.
Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in the Liolaemus montanus group (Squamata: Liolaemidae)

Integrative taxonomy (IT) is becoming a preferred approach to delimiting species boundaries by including different empirical criteria. IT methods can be divided into two types of procedures both of which use multiple kinds of evidence: step-by-step approaches test hypotheses by sequential evaluation in a hypothetic-deductive framework, while model-based procedures delimit groups based on statistical information criteria. In this study we used a step-by-step approach and a Gaussian clustering (GC) method to test species boundaries in the northernmost species of the Liolaemus montanus group. We used different methods based on mitochondrial and nuclear DNA sequence data, morphological measures and niche envelope variables. In contrast with GC, our step-by- step approach shows that one Andean population (Abra Apacheta) previously considered part of L. melanogaster, is actually nested within another clade; another Andean species, L. thomasi, is equivocally shown to be either a distinct species or conspecific with L. ortizi; and an additional Andean population (Abra Toccto) is delimited by concordance among most lines of evidence and different methods as a distinct lineage. However, one of the oldest and low-elevation populations (Nazca) is strongly delimited by all data sets and IT procedures as a new lineage distinct from any currently recognized species.
Molecular characterisation of the polyhistidine triad proteins of Streptococcus pneumoniae.

v Declaration . vii Abbreviations . ix Acknowledgements . xi Chapter 1: Introduction . 1 1.1 Significance of Streptococcus pneumoniae for human health . 1 1.2 Pathogenesis of pneumococcal disease and underlying molecular mechanisms . 1 1.2.1 Colonisation . 2 1.2.2 Progression to invasive disease . 3 1.2.3 Host immune response to pneumococci . 3 1.3 Treatment and prevention of pneumococcal disease. 4 1.3. 1 Antibiotics . 4 1.3. 2 Vaccines in current use and their limitations . 5 1.3. 3 Alternative vaccination strategies . 6 1.3. 4 Protein-based vaccines . 8 1.4 Protein vaccine candidates . 9 1.4. 1 Pneumolysin . 9 1.4. 2 Pneumococcal surface protein A (PspA) . 10 1.4. 3 Pneumococcal surface protein C (PspC) . 11 1.4. 4 Pneumococcal surface adhesin A (PsaA) . 11 1.4. 5 Combination vaccines. 12 1.5 Polyhistidine triad proteins . 12 1.5. 1 Structural features of Pht proteins . 13 1.5. 2 Genetic organisation and regulation of expression of pht genes . 15 1.5. 3 Use in vaccines . 16 1.5. 4 Roles and functions of Pht proteins in pathogenesis . 19 1.6 Zinc homeostasis in S. pneumoniae . 22 1.6. 1 Requirement for zinc and its import and export . 22 1.6. 2 Mechanism of zinc toxicity . 23 1.7 Project aims . 24 Chapter 2: Materials and Methods . 27 2.1 Strains and plasmids . 27 2.2 Growth media . 29 2.3 Oligonucleotide primers. 29 2.4 Manipulation of DNA . 32 2.4. 1 PCR, agarose gel electrophoresis and DNA sequencing . 32 2.4. 2 Restriction digestion and ligation . 33 2.5 Transformation of bacteria . 33 2.5. 1 THY method for pneumococcal transformation . 33 2.5. 2 Preparation of pneumococcal competent cells and back transformation . 33 2.5. 3 Preparation of competent E. coli and transformation . 34 2.6 Expression and purification of proteins . 34 2.6. 1 Expression of pneumococcal proteins . 34 2.6. 2 Purification of pneumococcal proteins . 34 2.6. 3 Cloning, expression and purification of factor H and SCR domain proteins . 35 2.7 Enzyme-linked immunosorbent assay . 36 2.8 Surface plasmon resonance . 36 2.9 Flow cytometry . 37 2.10 Preparation of bacterial lysates and precipitation of proteins from culture supernatants . 37 2.11 Cell wall digestion assay . 38 2.12 Assay for release of PhtD over time . 38 2.13 SDS-PAGE and Western blotting . 38 2.14 Inductively coupled plasma mass spectrometry . 39 2.14. 1 Purified proteins . 39 2.14. 2 Pneumococcal cultures . 39
Comparative ultrastructural analysis of Chloromonas and Gloeomonas (Chlorophyceae): tracing the origin of Gloeomonas-specific basal apparatus traits

Abstract: On the basis of prior phylogenetic analyses placing Gloeomonas as a lineage within the very diverse genus Chloromonas, it was hypothesized that the morphologically distinct Gloeomonas, bearing widely spaced basal bodies, evolved from ancestral organisms like Chloromonas. In addition, the phylogenetically related Chloromonas (Cr.) rubrifilum, was expected to possess traits intermediate to the two forms. To test these hypotheses, we performed detailed transmission electron microscope analysis on nine species of these genera. The species were divided into two categories on the basis of ultrastructural features: group 1, consisting of four diverse species of Chloromonas and Ixipapillifera, had a V-shaped basal body arrangement, and group 2, of Cr. rubrifilum and four Gloeomonas species, forming a single clade possessing widely spaced basal bodies. Members of group 1 commonly had a simple, flat plate-like distal connecting fiber (dcf), three or sometimes two microtubules in the sinister root, continuous dexter and sinister striated microtubule-associated fibers (SMAFs), and a coarsely striated proximal fiber (CSPF) at the posterior-most regions of the basal bodies and probasal bodies, but lacked proximal and median proximal connecting fibers. Group 2 inherited these features, but had novel traits including the elongation and modification of the dcf, SMAFs, and CSPF that occurred with separation of basal bodies during growth, a dcf-associated layered structure, as well as protruding flagellar collars. The ultrastructural traits of Gloeomonas are interpreted as being evolutionarily modified from an ancestral Chloromonas morphology. Specific ultrastructural features were determined to be useful in characterizing these genera. Cr. rubrifilum of group 2 was not intermediate morphologically, but possessed the traits of Gloeomonas; thus G. rubrifilum comb. nov. was proposed.
Determinação da composição química e dos valores de energia metabolizável de alguns alimentos proteicos para frangos de corte

We conducted a biological assay using the traditional method of excreta collection, with the purpose to determine the values of apparent metabolizable energy, apparent metabolizable energy corrected for nitrogen balance, and the chemical composition of six feeds: deactivated whole soybean with shuck; deactivated whole soybean without shuck; soy protein concentrate; extruded semi-whole soybean meal; soybean meal; and wheat gluten. We used 252 chicks of the Cobb 500 commercial lineage, from 14 to 24 days of age, distributed in a completely randomized design, with seven treatments (six test rations and a reference ration) and six repetitions with six birds per experimental unit. The five initial days were destined to the adaptation of the birds to the experimental rations, and the five final days were destined to excreta collection, which was carried out twice a day. The values of apparent metabolizable energy corrected for nitrogen balance, based on natural matter determined in broiler chicken aged from 14 to 24 days old were as follows: deactivated whole soybean with shuck: 2797 kcal/kg; deactivated whole soybean without shuck: 3012 kcal/kg; soy protein concentrate:, 2554 kcal/ kg; extruded semi-whole soybean meal: 2467 kcal/kg; soybean meal: 2221 kcal/kg and wheat gluten: 3813 kcal/kg. Keywords: deactivated whole soybean; extruded semi-whole soybean meal; soy protein concentrate; soybean meal; wheat gluten.
EFFECTS OF PACKAGE ATMOSPHERE AND TEMPERATURE ON PHENOLICS, TOTAL ANTIOXIDANT CAPACITY AND COLOUR IN KERNELS OF 'FRANQUETTE' WALNUTS DURING 8-MONTH STORAGE

The effects of package atmosphere and temperature on phenolic compounds, total antioxidant capacity and colour were investigated in kernels of 'Franquette' walnuts stored for up to 8 months. Dried walnuts were sealed under air or 100% N 2 and stored at 1°C or 20°C. The highest total phenolics concentration (25.41 mg gallic acid equivalents g -1 ) and total antioxidant capacity (185.6 μmol trolox equivalents g -1 , and 174.2 μmol trolox equivalents g -1 according to FRAP and DPPH method, respectively) were observed in samples before storage. The above parameters decreased progressively during storage. Low temperature and N 2 -atmosphere inhibited decline while their combination provided best preservation of nutritional value. Additive effects of low temperature and N 2 -atmosphere were also observed in retention of L * and hue angle colour parameters while Chroma was affected only by temperature. Major phenolic compounds were ellagic, protocatechuic, vanillic, and syringic acids and found at concentrations of 822.4 μg g -1 , 581.8 μg g -1 , 581.6 μg g -1 , and 310.2 μg g -1 , respectively. At the end of storage all phenolic compounds decreased and the decrease was most pronounced in air at 20°C (54% of all compounds, in average) and less in N 2 -atmosphere at 1°C (18% of all compounds, in average).
Morpho-physiological evaluation of groundnut (Arachis hypogaea L.) genotypes for iron deficiency tolerance.

Iron deficiency is one of the major yield limiting factors in groundnut. The soils of Pothwar (90% of groundnut production area in Pakistan) are calcareous in nature, thus groundnut is exposed to Fe deficiency. Seeds of 20 varieties/ advance breeding lines of groundnut were collected to evaluate Fe deficiency responses. Seeds were germinated in pots with 1:1 soil to sand ratio with added recommended NPK fertilizer. Fe-EDTA (0.1mmol/L) was supplemented as foliar spray to control plants, however, no additional Fe was applied to Fe deficient plants. Physiological parameters such as chlorophyll content, active and total Fe concentrations were recorded for each genotype under Fe deficient and Fe sufficient conditions. Morphological parameters including pods per plant, pod weight per plant, seeds per plant and seed weight per plant were recorded at harvesting. Genotypes were ranked by multivariate cluster analysis. Data showed that BARI-2000 and Chakori were among the Fe stress tolerant genotypes while Golden and Lisn were among the Fe deficiency intolerant genotypes. Relative values for SPAD values ranged from 60.50% in 2KCG020 to 87. 8% in BARI-2000. Total Fe concentration was 48.8%in Lisn and 66.5% in BARI-2000. Relative value of biomass produced by Chakori and Golden was 85.5% and 66.3%, respectively. The genotypes ranked best on the basis of morpho-physiological parameters will be helpful for making recommendations to groundnut farmers of the Pothwar region.
The seasonal quantitative distribution of coliform germs in the Arieş river (Romania) water affected by pollution.

Faecal pollution of river water can lead to health problems because of the presence of infectious microorganisms. These may be derived from human sewage or animal sources. Water safety or quality is best described by a combination of sanitary inspection and microbial water quality assessment. This approach provides data on possible sources of pollution in Aries river water, as well as numerical information on the actual level of faecal pollution according with the analzyed bacteriological parameters.
Delivery of an Adeno-Associated Virus Vector into Cerebrospinal Fluid Attenuates Central Nervous System Disease in Mucopolysaccharidosis Type II Mice.

Mucopolysaccharidosis type II (MPS II) is a rare X-linked genetic disorder caused by deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS), leading to impaired catabolism of ubiquitous polysaccharides and abnormal accumulation of these undegraded substrates in the lysosome. Like many lysosomal storage diseases, MPS II is characterized by both somatic and central nervous system (CNS) involvement. Intravenous enzyme replacement therapy can improve somatic manifestations of MPS II, but systemic IDS does not cross the blood–brain barrier and therefore cannot address CNS disease. In this study, an adeno-associated virus serotype 9 vector carrying the IDS gene was injected into the cerebrospinal fluid (CSF) of IDS deficient mice, a model of MPS II. Treated mice exhibited dose-dependent IDS expression and resolution of brain storage lesions, as well as improvement in long-term memory in a novel object recognition test. These findings suggest that delivery of adeno-associated virus vectors into CSF could.
Using multiple tracers and directly accounting for trophic modification improves dietary mixing‐model performance

Stable isotope (SI) mixing models are one of the most common approaches used to infer resource pathways in consumers. However, SIbased analyses are often underdetermined, and consumer SI fractionation is often unknown. The use of fatty acid (FA) biomarkers in mixing models offers an alternative approach that can resolve the underdetermined constraint. A limitation to both methods is the considerable uncertainty regarding the “trophic modification” of dietary tracers, which occurs when consumers transform dietary resources into their own tissues. We tested the utility of SI and FA approaches for inferring the diets of the marine benthic isopod (Idotea wosnesenskii) fed various marine macroalgae in controlled feeding trials. Our analyses quantified how the accuracy and precision of Bayesian mixing models were influenced by the choice of algorithm (SIAR vs. MixSIR), trophic modification (assumed or known), and whether the model was under or overdetermined (seven sources and two vs. 26 tracers) for cases where isopods were fed an exclusive diet of one of the seven macroalgae. Using the conventional approach (two SI with assumed trophic modification) resulted in average model outputs, that is, the contribution from the exclusive resource =0.20 ± 0.23 (0.00–0.79), mean ± SD (95% credible interval), that only differed slightly from the prior assumption. This result was only somewhat improved by the use of measured trophic modification values for SI data. Using the FAbased approach with known trophic modification greatly improved model performance, that is, the contribution from the exclusive resource =0.91 ± 0.10 (0.58–0.99). The choice of algorithm (SIAR vs. MixSIR) made a clear difference when trophic modification was known, and the model was overdetermined. In this case, SIAR and MixSIR had outputs of 0.86 ± 0.11 (0.48–0.96) and 0.96 ± 0.05 (0.79–1.00), respectively. When using FA biomarkers, going from two to seven tracers dramatically improved model performance (i.e., from 0.55 to 0.89, respectively), whereas going from 13 to 26 tracers only improved performance by 0.01. This analysis shows the choice and number of dietary tracers and the trophic modification assumption greatly influence the performance of mixingmodel dietary reconstructions and ultimately our understanding of what resources actually support aquatic consumers.
Adaptive Behavior and Executive Functioning in Children with Neurofibromatosis Type 1 Using a Mixed Design.

OBJECTIVE Children with neurofibromatosis type 1 (NF1) demonstrate poorer adaptive functioning compared with same-aged peers; however, there is limited research about the longitudinal pattern of adaptive behavior. The aim of this investigation was to examine parent-reported adaptive behavior of children with NF1 longitudinally beginning in early childhood and to examine relations with executive functioning. METHOD Children with NF1 were assessed during early childhood (n = 59; aged 3-7; mean = 4.8, SD = 1.42) or school age (n = 39; aged 9-13; mean = 10.85, SD = 1.58), and a subset was seen at both time points (n = 26). The Scales of Independent Behavior-Revised was used to assess adaptive functioning, and the Behavior Rating Inventory of Executive Function-Preschool Version/Behavior Rating Inventory of Executive Function was used to evaluate everyday executive functioning. RESULTS Adaptive behavior in early childhood was significantly correlated with adaptive behavior at school age (with the exception of social interaction and communication skills) and was significantly poorer at school age. The frequency of difficulties increased over time for overall adaptive behavior and motor skills. Executive functioning was related to adaptive behavior cross-sectionally within early childhood and at school age and showed longitudinal predictive value over time. CONCLUSION This research contributes to the limited NF1 adaptive behavior literature by characterizing the longitudinal pattern of adaptive behavior and relations with executive abilities.
Emerging roles for non-selenium containing ER-resident glutathione peroxidases in cell signaling and disease

Abstract Maintenance of cellular redox control is pivotal for normal cellular functions and cell fate decisions including cell death. Among the key cellular redox systems in mammals, the glutathione peroxidase (GPX) family of proteins is the largest conferring multifaceted functions and affecting virtually all cellular processes. The endoplasmic reticulum (ER)-resident GPXs, designated as GPX7 and GPX8, are the most recently added members of this family of enzymes. Recent studies have provided exciting insights how both enzymes support critical processes of the ER including oxidative protein folding, maintenance of ER redox control by eliminating H2O2, and preventing palmitic acid-induced lipotoxicity. Consequently, numerous pathological conditions, such as neurodegeneration, cancer and metabolic diseases have been linked with altered GPX7 and GPX8 expression. Studies in mice have demonstrated that loss of GPX7 leads to increased differentiation of preadipocytes, increased tumorigenesis and shortened lifespan. By contrast, GPX8 deficiency in mice results in enhanced caspase-4/11 activation and increased endotoxic shock in colitis model. With the increasing recognition that both types of enzymes are dysregulated in various tumor entities in man, we deem a review of the emerging roles played by GPX7 and GPX8 in health and disease development timely and appropriate.