Miracle-dz/UniFAR-FTUs huggingface dataset:
The relevance of glycine and serine in poultry nutrition: a review

ABSTRACT 1. Dietary glycine equivalents (Glyequi) for glycine and serine represent the first-limiting non-essential amino acid in poultry diets. Targeted adjustment of essential amino acids and Glyequi in diets can considerably decrease crude protein (CP) in poultry diets below the limit of CP reduction when only essential amino acids are adjusted. 2. The level to which CP can be reduced in diets adequate in Glyequi depends on the objective; which includes reducing dietary CP without affecting performance and increasing nitrogen utilisation efficiency. Dietary CP can be reduced to ~15–16% in diets for up to 21 d old broiler chicken without affecting growth performance compared to responses to diets with currently common CP concentrations by considering Glyequi in the diet formulation. Dietary CP can be further reduced to maximise nitrogen utilisation efficiency; however, this leads to reduced growth performance. 3. The dietary Glyequi requirement of poultry varies depending on other dietary constituents. In broiler chickens up to 21 days of age, the dietary Glyequi requirement is estimated to be between 11 and 20 g/kg. This estimate is influenced by the concentrations of Cys and the endogenous Glyequi precursors, threonine and choline. Urinary nitrogen excretion seems to be a major determinant of the response to dietary Glyequi, because it is needed for uric acid formation. 4. The variable requirement for dietary Glyequi means that its static recommendation in poultry diets would lead to high safety margins in Glyequi supply or the risk of Glyequi deficiency. Variable recommendations for dietary Glyequi concentrations would help to supply birds based on their specific requirements and could reduce nitrogen emissions originating from poultry farming.
The Effect of Variations in Force Feedback in a Virtual Reality Environment on the Performance and Satisfaction of Dental Students

Introduction The aim of this study was to investigate the transfer of skills between various levels of force feedback (FFB) using the Simodont dental trainer (Moog, Nieuw-Vennep, the Netherlands). Students practiced a manual dexterity exercise in a virtual reality environment at a standard level of FFB and then were tested at the standard and an altered level of FFB. In addition, the students' satisfaction with the training exercise was evaluated. Methods One hundred twenty-six first-year dental students were randomly distributed into four groups and underwent a manual dexterity test in the virtual reality environment with automatic assessment after a 3-month period of practicing with standard FFB. The test consisted of drilling with the standard FFB and an altered level of FFB to evaluate the effect on performance. After the test, the participants completed a questionnaire. Results The results showed that 74% of the students who passed completed between one of three and three of three successful attempts at FFB levels at which they had not previously practiced. Conclusions The results of this study imply that if students practice a sufficient amount of time at one level of FFB, a skill is transferable from one level of FFB to another.
Weight among children born 2005-2011 in Nuuk at the time of school entry

ABSTRACT The aim of this study was to explore weight status among children born between 2005–2011 at the time of their school entry in Nuuk, and separately to compare weight status between Nuuk and the rest of Greenland among children born in 2011. Study method was an observational study based on data from the electronic medical records (EMR). All children born between 2005–2011 with an address in Nuuk, and registered weight and height were included. For children born in 2011 two study populations were used: children living in Nuuk, and children living outside Nuuk. Body Mass Index (BMI) was calculated. Atotal of 1,616 children born in 2005–2011, with address in Nuuk between 2011-2017 were identified. 78% were included (N = 1, 280: 676 boys and 604 girls, ranging from 5.4–7.6 years). Prevalence of overweight and obesity were estimated to 12.0% (N = 153) and 5.1% (N = 65)respectively. Among children born in 2011, the prevalence of overweight or obesity was 14.6% in Nuuk, compared to 28.8% in the rest of Greenland (p < 0.001). The prevalence of overweight and obesity was stable for children living in Nuuk. A higher prevalence was observed among children living outside Nuuk. Continued monitoring of weight status is recommended. Abbreviations: BMI: body mass index; EMR: electronic medical records; IOTF: international obesity task force; SD: standard derivation
The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics

Abstract A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3′ overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson–Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions

Abstract Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein–protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts emanate from the main chain or side chain. We tested the score on 174 native interactions for which 100 decoys each were constructed using ZDOCK. The native structure scored better than any of the decoys in 146 cases and was able to rank within the 95th percentile in 162 cases. This easily outperforms a competing method, CIPS. We also benchmarked our scoring scheme on 15 targets from the CAPRI dataset and found that our method had results comparable to that of CIPS. Further, our method is able to analyse higher order protein complexes without the need to explicitly identify chains as receptors or ligands. The PIZSA server is easy to use and could be used to score any input three-dimensional structure and provide a residue pair-wise break up of the results. Attractively, our server offers a platform for users to upload their own potentials and could serve as an ideal testing ground for this class of scoring schemes.
Predicted values for closing volumes using a modified single breath nitrogen test.

The measurement of closing volumes has been proposed as a simple and sensitive test of small airway function. Prediction formulas for closing volumes, obtained from a large number of asymptomatic, nonsmoking adults have not thus far been reported. Closing volumes were measured in 284 asymptomatic, nonsmoking adults using a modification of the single breath nitrogen test. Data from these subjects were then used to derive prediction formulas for closing volume expressed as a percentage of vital capacity and for closing capacity expressed as a percentage of total lung capacity. These formulas confirmed the findings of others that closing volumes appear to increase linearly with age, presumably because of loss in lung elastic recoil. The advantages of the modified single breath nitrogen test are (1) it is suitable for use as a screening test and in epidemiologic studies because it does not require equipment that is either extremely costly or technically difficult to operate; (2) it can be used to compute tota.
A dual role of the ribosome-bound chaperones RAC/Ssb in maintaining the fidelity of translation termination

Abstract The yeast ribosome-associated complex RAC and the Hsp70 homolog Ssb are anchored to the ribosome and together act as chaperones for the folding and co-translational assembly of nascent polypeptides. In addition, the RAC/Ssb system plays a crucial role in maintaining the fidelity of translation termination; however, the latter function is poorly understood. Here we show that the RAC/Ssb system promotes the fidelity of translation termination via two distinct mechanisms. First, via direct contacts with the ribosome and the nascent chain, RAC/Ssb facilitates the translation of stalling-prone poly-AAG/A sequences encoding for polylysine segments. Impairment of this function leads to enhanced ribosome stalling and to premature nascent polypeptide release at AAG/A codons. Second, RAC/Ssb is required for the assembly of fully functional ribosomes. When RAC/Ssb is absent, ribosome biogenesis is hampered such that core ribosomal particles are structurally altered at the decoding and peptidyl transferase centers. As a result, ribosomes assembled in the absence of RAC/Ssb bind to the aminoglycoside paromomycin with high affinity (KD = 76.6 nM) and display impaired discrimination between stop codons and sense codons. The combined data shed light on the multiple mechanisms by which the RAC/Ssb system promotes unimpeded biogenesis of newly synthesized polypeptides.
MiR-122-3p regulates the osteogenic differentiation of mouse adipose-derived stem cells via Wnt/β catenin signaling pathway.

OBJECTIVE To explore the regulatory mechanism of micro-ribonucleic acid (miR)-122-3p in the osteogenic differentiation of mouse adipose-derived stem cells (mADSCs). MATERIALS AND METHODS The regulatory mechanism of miR-122-3p in the osteogenic differentiation of mesenchymal stem cells was investigated through its overexpression and knockdown. RESULTS The overexpression of miR-122-3p inhibited the osteogenic differentiation of mADSCs. On the contrary, its knockdown promoted the osteogenic differentiation of mADSCs. The further study on the molecular mechanism of miR-122-3p regulating mADSCs' osteogenic differentiation showed that the overexpression of miR-122-3p could activate the Wingless and int-1 (WNT)/β-catenin signaling pathway, but the knockdown of miR-122-3p could repress this signaling pathway. CONCLUSIONS MiR-122-3p influences the osteogenic differentiation of mADSCs by modulating the WNT/β-catenin signaling pathway.
Substance P enhances BMSC osteogenic differentiation via autophagic activation

Bone mesenchymal stem cells (BMSCs) are the most commonly investigated progenitor cells in bone tissue engineering for treating severe bone defects. Strategies for regulating BMSC differentiation fate have received wide attention, in which redox homeostasis plays an important role due to the change in energy metabolism during stem cell differentiation. In the present study, it was observed that autophagic activity was induced along with BMSC osteogenic differentiation and subsequently regulated reactive oxygen species (ROS) generation and the level of osteogenesis. Furthermore, it was also observed that neuropeptide substance P (SP) administration could enhance the autophagic activity in rat BMSCs via the AMPK and mTOR pathways, as well as decreasing ROS generation and promoting osteogenic differentiation. Inhibition of autophagic activity by 3-MA reversed the effects of SP on ROS and osteogenic levels. The present results indicated that autophagic activity participated in the regulation of differentiation fate of BMSCs and SP could promote osteogenic differentiation by activating autophagy, providing a more precise biological mechanism for its application in bone tissue engineering.
Phononic Crystals for Shaping Fluids

Surface acoustic waves (SAWs) generated on piezoelectric materials have been used as a convenient method for microfl uidic manipulation, where microliter volumes of liquids are actuated by their interaction with sound waves. A wide range of fundamental fl uid actuations, including droplet movement, mixing, splitting, nebulization, and centrifugation, have been performed on such a piezoelectric surface. [ 1 , 2 ] Mention of the jetting of a sessile drop from a piezoelectric substrate have been made in reports on other phenomenon, where the propagating SAW is refracted into the liquid and jets a droplet in a direction known as the Rayleigh angle. [ 3 , 4 ] More signifi cantly, it has also been reported that, by using two circular single-phase unidirectional transducers to radiate the SAW, the energy can be focused to deform a drop into an interfacial jet perpendicular to the piezoelectric surface. [ 5 ]
Pyruvate Kinase of Streptococcus lactis

The kinetic properties of pyruvate kinase (ATP:pyruvate-phosphotransferase, EC 2.7.1.40) from Streptococcus lactis have been investigated. Positive homotropic kinetics were observed with phosphoenolpyruvate and adenosine 5′-diphosphate, resulting in a sigmoid relationship between reaction velocity and substrate concentrations. This relationship was abolished with an excess of the heterotropic effector fructose-1,6-diphosphate, giving a typical Michaelis-Menten relationship. Increasing the concentration of fructose-1,6-diphosphate increased the apparent Vmax values and decreased the Km values for both substrates. Catalysis by pyruvate kinase proceeded optimally at pH 6.9 to 7.5 and was markedly inhibited by inorganic phosphate and sulfate ions. Under certain conditions adenosine 5′-triphosphate also caused inhibition. The Km values for phosphoenolpyruvate and adenosine 5′-diphosphate in the presence of 2 mM fructose-1,6-diphosphate were 0.17 mM and 1 mM, respectively. The concentration of fructose-1,6-diphosphate giving one-half maximal velocity with 2 mM phosphoenolpyruvate and 5 mM adenosine 5′-diphosphate was 0.07 mM. The intracellular concentrations of these metabolites (0.8 mM phosphoenolpyruvate, 2.4 mM adenosine 5′-diphosphate, and 18 mM fructose-1,6-diphosphate) suggest that the pyruvate kinase in S. lactis approaches maximal activity in exponentially growing cells. The role of pyruvate kinase in the regulation of the glycolytic pathway in lactic streptococci is discussed.
Anticytokine autoantibodies leading to infection: early recognition, diagnosis and treatment options

Purpose of review The current review gives a concise and updated overview of the relative new field of anticytokine autoantibodies (ACAA) and associated infections with a focus on recent findings regarding clinical manifestions, diagnostic and treatments. Recent findings Several recent case reports of unusual presentations of patients with neutralizing autoantibodies to IFN-γ and granulocyt macrophage colony-stimulating factor and expand the spectrum of clinical manifestations and suggest that anticytokine-mediated acquired immunodeficiency causing susceptibility to infection may be underdiagnosed. There is an expanding geographical distribution of antigranulocyt macrophage colony-stimulating factor associated Cryptococcus gattii infection. The spectrum of identified infections in patients with neutralizing antibodies to IFN-γ has a strong endemic component. Rituximab or cyclophophamide in addition to antimycobacterials could be a treatment options in refractory cases. NF-κB2 deficiency may be associated with a complex pattern of high titre neutralizing ACAA similar to autoimmune polyglandular syndrome type I and Thymoma. New technique for the detection of anticytokine antibodies are presented. Quantiferon testing, which is widely available for TB-diagnostic, may be repurposed to detect anti-IFN-γ autoantibodies. We propose that this test could be as well used to show if they are neutralizing. Summary ACAA are an emerging cause of acquired immunodeficiency which is likely underdiagnosed. Recent case reports document expanding spectra of clinical manifestations. NF-κB2 deficiency may be associated with a complex anti cytokine autoantibody pattern.
One hundred years after the 1918 pandemic: new concepts for preparing for influenza pandemics.

PURPOSE OF REVIEW In the 100 years since the influenza pandemic of 1918-1919, the most deadly event in human history, we have made substantial progress yet we remain vulnerable to influenza pandemics This article provides a brief overview of important advances in preparing for an influenza pandemic, viewed largely from the perspective of the healthcare system. RECENT FINDINGS We have gained insights into influenza pathogenicity, the animal reservoir and have improved global surveillance for new strains and tools for assessing the pandemic risk posed by novel strains. Public health has refined plans for severity assessment, distribution of countermeasures and nonpharmaceutical approaches. Modest improvements in vaccine technology include cell culture-based vaccines, adjuvanted vaccine and recombinant technology. Conventional infection control tools will be critical in healthcare settings. New evidence suggests that influenza virus may be present in aerosols; the contribution of airborne transmission and role of N95 respirators remains unknown. Baloxavir and pimodivir are new antivirals that may improve treatment, especially for severely ill patients. Optimal use and the risk of resistance require further study. SUMMARY Despite the progress in pandemic preparedness, gaps remain including important scientific questions, adequate resources and most importantly, the ability to rapidly deliver highly effective vaccines.
Input-output analysis of high-speed axisymmetric isothermal jet noise

We use input-output analysis to predict and understand the aeroacoustics of high-speed isothermal turbulent jets. We consider axisymmetric linear perturbations about Reynolds-averaged Navier-Stokes solutions of ideally expanded turbulent jets with jet Mach numbers 0.6 < Mj < 1.8. For each base flow, we compute the optimal harmonic forcing function and the corresponding linear response using singular value decomposition of the resolvent operator. In addition to the optimal mode, input-output analysis also yields sub-optimal modes associated with smaller singular values. For supersonic jets, the optimal response closely resembles a wavepacket in both the near-field and the far-field such as those obtained by the parabolized stability equations (PSE), and this mode dominates the response. For subsonic jets, however, the singular values indicate that the contributions of sub-optimal modes to noise generation are nearly equal to that of the optimal mode, explaining why the PSE do not fully capture the far-fiel.
Visual Performance in the "Real World": Contrast Sensitivity, Visual Acuity, and Effects of Macular Carotenoids.

We compare visual acuity (VA) to contrast sensitivity (CS) testing in assessing "real-world" visual performance and recommend that both should be measured routinely in the clinic. A new model to improve our understanding of the visual impact created by changes in CS is presented. The role of nutritional intervention in improving visual performance is reviewed and emphasized. A brief history and illustration of both VA and CS, within the scope of visual performance, is presented. Parameters for effective CS testing in the clinic, and guidelines for interpretation of results, including a new model for understanding the visual impact of changes in CS, are also presented. Relevant research that supports the use of the macular carotenoids lutein, zeaxanthin, and meso-zeaxanthin to enhance visual performance is reviewed with suggested guidelines for supplementation. CS testing is easily performed at a single intermediate target size and is an excellent tool for accurate assessment of a patient's overall visual experience. Research continues to uncover the strong link between nutrition and visual performance; the macular carotenoids appear to be especially effective in this regard, and their benefits to visual performance now importantly include contrast sensitivity. Clinicians can provide an improved level of care by incorporating into the examination protocol CS testing and, where appropriate, nutritional counseling and intervention. This article is protected by copyright. All rights reserved.
The Selective Rat Toxicant Norbormide Blocks KATP Channels in Smooth Muscle Cells But Not in Insulin-Secreting Cells

Norbormide is a toxicant selective for rats to which it induces a widespread vasoconstriction. In a recent paper, we hypothesized a role of ATP-sensitive potassium (KATP) channels in norbormide-induced vasoconstriction. The current study was undertaken to verify this hypothesis by comparing the effects of norbormide with those of glibenclamide, a known KATP channel blocker. The whole-cell patch-clamp method was used to record KATP currents in myocytes freshly isolated from the rat and mouse caudal artery and from the rat gastric fundus, as well as in insulin-secreting pancreatic beta cells (INS-1 cells). Smooth muscle contractile function was assessed on either rat caudal artery rings or gastric fundus strips. Molecular modeling and docking simulation to KATP channel proteins were investigated in silico. Both norbormide (a racemic mixture of endo and exo isomers) and glibenclamide inhibited KATP currents in rat and mouse caudal artery myocytes, as well as in gastric fundus smooth muscle cells. In rat INS-1 cells, only glibenclamide blocked KATP channels, whereas norbormide was ineffective. The inhibitory effect of norbormide in rat caudal artery myocytes was not stereo-specific as both the endo isomers (active as vasoconstrictor) and the exo isomers (inactive as vasoconstrictor) had similar inhibitory activity. In rat caudal artery rings, norbormide-induced contraction was partially reverted by the KATP channel opener pinacidil. Computational approaches indicated the SUR subunit of KATP channels as the binding site for norbormide. KATP channel inhibition may play a role in norbormide-induced vasoconstriction, but does not explain the species selectivity, tissue selectivity, and stereoselectivity of its constricting activity. The lack of effect in INS-1 cells suggests a potential selectivity of norbormide for smooth muscle KATP channels.