Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination

LNX (Ligand of Numb Protein-X) proteins, LNX1 and LNX2, are RING- and PDZ-based E3-ubiquitin ligases known to interact with Numb. Silencing of LNX2 has been reported to down-regulate WNT and NOTCH, two key signaling pathways in tumorigenesis. Here we report the identification of the domain boundary of LNX2 to confer its ubiquitination activity, its crystal structure along with functional studies. We show that the RING domain in LNX2 is flanked by two Zinc-binding motifs (Zn-RING-Zn), in which the N-terminal Zinc-binding motif adopts novel conformation. Although this motif follows the typical Cys2His2-type zinc finger configuration, it is devoid of any secondary structure and forms an open circle conformation, which has not been reported yet. This unique N-terminal Zn-finger motif is indispensable for the activity and stability of LNX2, as verified using mutational studies. The Zn-RING-Zn domain of LNX2 is a dimer and assumes a rigid elongated structure that undergoes autoubiquitination and undergoes N-terminal polyubiquitination. The ubiquitin chains consist of all seven possible isopeptide linkages. These results were validated using full-length LNX2. Moreover we have demonstrated the ubiquitination of cell fate determinant protein, Numb by LNX2. Our study provides a structural basis for the functional machinery of LNX2 and thus provides the opportunity to investigate suitable drug targets against LNX2.
Defining operational taxonomic units using DNA barcode data

Abstract The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene ‘for’ speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to ‘species’, and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.
Dietary requirements of leucine, isoleucine, and valine in male broilers during the starter period.

Growth studies were conducted with 3-wk-old, male broiler chicks to determine their requirements for the branched-chain amino acids (BCAA) leucine, isoleucine, and valine during the starter period. The central-composite, rotatable design was applied. The data were analyzed using regression methodology. The results showed that the linear term of Leu and the cross-product terms of Leu with Ile or Val were nonsignificant (P greater than .05). Second-order equations described the relationship between the BCAA, weight gain (WG), and feed conversion (FC). The coefficient of determination values indicated that 80% or more of the variation in WG and FC was explained by the polynomial equations. The results suggested that the Leu requirement does not exceed 1.16% of a diet calculated to contain 3,200 kcal of metabolizable energy per kilogram. The optimum response, maximum in the case of WG (444 g) and minimum for FC (1.40), would be obtained by feeding a diet containing 1.16, . 80, and . 90% of Leu, Ile, and Val, respectively. The values of Ile and Val are the actual values obtained when the diets were hydrolyzed for 72 hours. For Leu, however, the hydrolysis time was 24 hours.
Optimization of triacylglycerol and starch production in Chlamydomonas debaryana NIES-2212 with regard to light intensity and CO2 concentration.

Triacylglycerol (TAG) and starch produced by micro-algae are potential sources of biofuel. Our previous studies showed that the unicellular green alga, Chlamydomonas debaryana NIES-2212, which is a rare species of Chlamydomonas that possesses phosphatidylcholine (PC), is a seed organism for the development of biofuel producers. This alga accumulates large amounts of TAG and starch under completely photo-autotrophic conditions during stationary phase without nutrient deprivation. The present study was performed to optimize the growth conditions of this alga with regard to light intensity and CO2 concentration to improve the efficiency of TAG and starch production. The growth rate of C. debaryana was greater at higher light intensity, although there was no significant difference in the final cell density of the culture. The highest contents of TAG and starch, approximately 200 fmol cell-1 and 600 pg cell-1, respectively, were achieved with a light intensity of 200 µmol m-2 s-1 bubbled with air containing 5.0 % CO2. These results suggest that optimization of light intensity and CO2 concentration can enhance the productivity of TAG and starch by C. debaryana NIES-2212.
Incidence of parthenogenesis in eggs of various strains and varieties of domestic turkeys, Meleagris gallopavo.

Abstract Since 1953 considerable work at this Station has been devoted to the study of parthenogenetic development in Beltsville Small White (BSW) turkey eggs. Most of the work dealt with the incidence of parthenogenesis as influenced by selection and by environmental factors. It also was of interest to determine how widespread this form of development was, and to what extent it occurred, in eggs of other varieties and strains of domestic turkeys. These tests involved a total of 3,048 unfertilized eggs from 116 young turkeys representing 9 different varieties, strains, and variety crosses. Three of the groups were secured from commercial sources, the remainder were from State experiment stations. None of the hens involved had been selected for a high incidence of parthenogenetic development. In conducting the parthenogenetic tests, the same general procedures were followed as those outlined by Olsen and Marsden (1953), i.e., eggs from virgin hens were incubated at .
Tightness of LP via Max-product Belief Propagation

We investigate the question of tightness of linear programming (LP) relaxation for finding a maximum weight independent set (MWIS) in sparse random weighted graphs. We show that an edge-based LP relaxation is asymptotically tight for Erdos-Renyi graph $G(n,c/n)$ for $c \leq 2e$ and random regular graph $G(n,r)$ for $r\leq 4$ when node weights are i.i. d. with exponential distribution of mean 1. We establish these results, through a precise relation between the tightness of LP relaxation and convergence of the max-product belief propagation algorithm. We believe that this novel method of understanding structural properties of combinatorial problems through properties of iterative procedure such as the max-product should be of interest in its own right.
Evaluating the bio-energy potential of groundnut shell and sugarcane bagasse waste composite

An assessment has been carried out on bio-coal briquettes from coal with sugarcane bagasse and coal with groundnut shell. Proximate analyses and elemental compositions of the coal and biomasses were determined. Different samples of briquettes were produced by blending varying composition of the coal with the biomasses in the ratio of 100:0; 90:10, 80:20, 70:30, 60:40, 50:50, 40:60 and 0: 100, using calcium carbonate as a desulfurizing agent and cassava starch as a binder. A manual hydraulically operated briquetting machine was used with the pressure kept at 5MPa. The results of the properties evaluated shows that biomass increases the burning efficiency of briquettes with increase in the biomass material, increasing combustion rate, faster ignition, producing lesser ash and fewer pollutants. Results obtained shows that the calorific value of briquettes produced from coal-groundnut shells and coal-sugarcane bagasse ranges from 16.94 - 20.81 and 17.31 – 21.03 MJ/kg respectively. The ignition time ranges from 6.9 – 12.5 minutes for coal-groundnut shells briquettes while that of coal-sugarcane bagasse ranges from 6.5 – 11.1 minutes. The bio-coal blends with sugarcane bagasse were better than that of groundnut shells. However, both sugarcane bagasse and groundnut shells produce bio-coal briquettes that are very efficient, providing sufficient heat as at the time necessary, generating less smoke and gases (e.g sulphur) that are harmful to environment, and generating less ash, as these have adverse effect during cooking.
Effect of dietary phosphorus levels on performance of turkey breeder hens.

One hundred 30-wk-old medium weight white Orlopp turkey breeder hens were equally divided into four treatment groups according to the level of available P in the diet (.15, .30, .50, and .70%, respectively). The P provided in the basal diet (.15% available, .35% total) was from cereal grains and soybean meal. No supplemental phosphate was added. During the 20-wk experiment, there were no differences in number of days required to come into lay and in subsequent egg production. Specific gravity, egg weight, number of shell pores, and body weight were similar under all treatments. The P levels of birds fed the four diets were 4.82, 4.93, 4.93, and 4.94 mg/100 mL, respectively, in serum and in femur were 15.8, 16.1, 16.8, and 16.4%, respectively. The P levels were slightly lower in birds fed the diet without added P. Excreta P levels (1.93, 2.49, 2.81, and 3.10%, respectively, in birds fed the four diets) were significantly (P less than .05) higher with each successive increase in dietary P. Hens fed diets containing . 50 or . 70% available P retained (46.9 and 54.8%, respectively) significantly more P than those fed diets containing . 15 or . 30% available P (28.1 and 33.8%, respectively). Fertility (76, 93, 90, and 89%, respectively) was significantly lower (P less than .05) from feeding the diet without added P. Hatchability rates of fertile eggs were similar for all treatments.
Reduced dietary phosphorus levels for layers.

Two experiments were undertaken to study the response of White Leghorn hens to low dietary phosphorus levels from 18 to 64 wk of age. A corn-soybean meal diet containing . 2% available phosphorus gave similar performance, up to 32 wk of age, as a similar control diet containing . 4% available phosphorus. Beyond 32 wk, although shell quality and average egg weight were similar, egg production was significantly reduced with the lower phosphorus diet. Phosphorus excretion (grams per bird per day) averaged . 47 g for . 4% vs . 28 g for . 2% available phosphorus when measured at 28 wk of age. In a second experiment identical procedures and bird number as used in Experiment 1 were employed with the exception that the test diet contained . 3% rather than . 2% available phosphorus. No differences were noted for any of the production variables measured between the . 4 and . 3% available phosphorus diets. Phosphorus excretion data collected at 25, 32, 44, and 60 wk of age showed a decrease of approximately 20% for hens receiving the lower phosphorus diet. Indeed the overall average for phosphorus excretion for the lower phosphorus diet was calculated to be identical to the 20% lower total phosphorus content of this diet (.59 vs .47%).
Changes and classification in myocardial contractile function in the left ventricle following acute myocardial infarction

In this research, we hypothesized that novel biomechanical parameters are discriminative in patients following acute ST-segment elevation myocardial infarction (STEMI). To identify these biomechanical biomarkers and bring computational biomechanics ‘closer to the clinic’, we applied state-of-the-art multiphysics cardiac modelling combined with advanced machine learning and multivariate statistical inference to a clinical database of myocardial infarction. We obtained data from 11 STEMI patients (ClinicalTrials.gov NCT01717573) and 27 healthy volunteers, and developed personalized mathematical models for the left ventricle (LV) using an immersed boundary method. Subject-specific constitutive parameters were achieved by matching to clinical measurements. We have shown, for the first time, that compared with healthy controls, patients with STEMI exhibited increased LV wall active tension when normalized by systolic blood pressure, which suggests an increased demand on the contractile reserve of remote functional myocardium. The statistical analysis reveals that the required patient-specific contractility, normalized active tension and the systolic myofilament kinematics have the strongest explanatory power for identifying the myocardial function changes post-MI. We further observed a strong correlation between two biomarkers and the changes in LV ejection fraction at six months from baseline (the required contractility (r = − 0.79, p < 0.01) and the systolic myofilament kinematics (r = 0.70, p = 0.02)). The clinical and prognostic significance of these biomechanical parameters merits further scrutinization.
Western diet induces colonic nitrergic myenteric neuropathy and dysmotility in mice via saturated fatty acid‐ and lipopolysaccharide‐induced TLR4 signalling

A high‐fat diet (60% kcal from fat) is associated with motility disorders inducing constipation and loss of nitrergic myenteric neurons in the proximal colon. Gut microbiota dysbiosis, which occurs in response to HFD, contributes to endotoxaemia. High levels of lipopolysaccharide lead to apoptosis in cultured myenteric neurons that express Toll‐like receptor 4 (TLR4). Consumption of a Western diet (WD) (35% kcal from fat) for 6 weeks leads to gut microbiota dysbiosis associated with altered bacterial metabolites and increased levels of plasma free fatty acids. These disorders precede the nitrergic myenteric cell loss observed in the proximal colon. Mice lacking TLR4 did not exhibit WD‐induced myenteric cell loss and dysmotility. Lipopolysaccharide‐induced in vitro enteric neurodegeneration requires the presence of palmitate and may be a result of enhanced NO production. The present study highlights the critical role of plasma saturated free fatty acids that are abundant in the WD with respect to driving enteric neuropathy and colonic dysmotility.
Subthalamic stimulation and neuropsychiatric symptoms in Parkinson’s disease: results from a long-term follow-up cohort study

Background Reports on behavioural outcomes after subthalamic nucleus deep brain stimulation in Parkinson’s disease are controversial and limited to short-term data. Long-term observation in a large cohort allows a better counselling and management. Methods To determine whether a long-term treatment with subthalamic stimulation induces or reduces impulse control behaviours, neuropsychiatric fluctuations and apathy, 69 patients treated with subthalamic stimulation are prospectively and retrospectively assessed using Ardouin Scale of Behavior in Parkinson’s Disease before and after 3–10 years of stimulation. Results At a mean follow-up of 6 years, all impulse control disorders and dopaminergic addiction were significantly decreased, apart from eating behaviour and hypersexuality. Neuropsychiatric fluctuations also significantly improved (ON euphoria: 38% of the patients before surgery and 1% after surgery, P<0.01; OFF dysphoria: 39% of the patients before surgery and 10% after surgery, P<0.01). However, apathy increased (25% of the patients after surgery and 3% before, P<0.01). With the retrospective analysis, several transient episodes of depression, apathy, anxiety and impulse control disorders occurred. Conclusions Bilateral subthalamic nucleus stimulation was overall very effective in improving impulse control disorders and neuropsychiatric fluctuations in parkinsonian patients in the long term despite a counteracting frequent apathy. Transient episodes of impulse control disorders still occurred within the follow-up. These findings recommend a close follow-up in parkinsonian patients presenting with neuropsychiatric symptoms before deep brain stimulation surgery. Clinical trial registration NCT01705418;Post-results.
The effect of mercury and vitamin E on tissue glutathione peroxidase activity and thiobarbituric acid values.

The effects of methyl mercuric chloride (CH3 HgCl) and mercuric chloride (HgCl2) on red blood cell (RBC), plasma, and liver glutathione peroxidase (GSH-Px) activities were determined in Japanese quail fed a semipurified diet with 1 ppm added selenium (Se). The RBC GSH-Px activity was significantly increased by 5 ppm mercury (Hg) as CH3 HgCl. Plasma GSH-Px activity was significantly depressed only in th 20 ppm Hg group. Liver GSH-Px activity was not affected. The RBC GSH-Px activity was significantly lower at all levels of HgCl2 compared to the Ch3 HgCl-treated birds. Plasma and liver GSH-Px activity of the HgCl2 -treated birds were not significantly different from control values. In a second experiment, GSH-Px activity and estimates of peroxidation via the thiobarbituric acid (TBA) test were determined on quail fed diets containing . 07 ppm added Se to which either 10 ppm Hg as CH3 HgCl or 150 ppm Hg as HgCl2 were added with or without the supplementation of vitamin E. Plasma and kidney GSH-Px activities were unaffected by CH3 HgCl, whereas RBC GSH-Px was significantly elevated. Kidney GSH-Px was significantly depressed by HgCl2-Vitamin E had no effect on GSH-Px activities. Vitamin E protected the liver, kidney, and brain from peroxidation; however, peroxidation was not induced by either of the mercurials.
The utilization of rye by growing chicks as influenced by calcium, vitamin D3, and fat type and level.

Four experiments were conducted with growing chicks to study the effects of feeding rye and wheat diets supplemented with different calcium levels, two types and two levels of fat, and increasing levels of vitamin D3 and to study the interrelationships of these dietary ingredients on chick performance. In Experiment 1, feed conversion efficiency was reduced to a much greater extend (10% vs. 1%) when tallow replaced soybean oil in a rye-based diet containing only . 6% calcium compared to a wheat-based diet. When the dietary calcium was increased to 1.1% the replacement of tallow by soybean oil resulted in only a small reduction in feed efficiency for chicks fed either the rye-(3%) or wheat- (1%) based diets. The retention of fat, particularly tallow, was depressed in rye as compared to wheat-fed birds. Fat retention was also influenced by calcium levels. Increasing the dietary calcium from . 6 to 1.1% improved tallow (16%) and depressed (7%) soybean oil retention in rye-based diets, whereas in wheat-based diets the retention for both fats was slightly decreased. Experiment 2 showed that the efficiency of utilization of rye diets containing 7.5% tallow was improved by 10% when the level of dietary calcium was increased from . 6 to 1.1% while the corresponding improvement in similarly formulated wheat diets was only 1%. The improvement of 2.5% fat, however, was only about 3% for both wheat and rye diets. The results from Experiment 3 showed that in the presence of a large excess of vitamin D3, the depression in the efficiency of utilization of the wheat diet was 13% but was less than 1% for the rye diet. This indicates that rye contains a factor that depresses vitamin D3 absorption. In Experiment 4, when dietary calcium was increased from . 80 to 2.00% or when penicillin (200 mg/kg) was added, the improvement in efficiency of feed utilization was greater in chicks fed a rye diet (7%) compared to those fed a wheat diet (1%). The rye diets, however, were always less efficiently utilized than the corresponding wheat diets. Vitamin D supplementation, in contrast, did not affect chick performance. These results show that the performance of chicks fed rye diets is markedly influenced by type and level of dietary fat and the level of dietary calcium.
Wearable Sensing of Cardiac Timing Intervals From Cardiogenic Limb Vibration Signals

In this paper, we describe a new method to measure aortic valve opening (AVO) and aortic valve closing (AVC) from cardiogenic limb vibrations (i.e., wearable ballistocardiogram (BCG) signals). AVO and AVC were detected for each heartbeat with accelerometers on the upper arm (A), wrist (W), and knee (K) of 22 subjects following isometric exercise. Exercise-induced changes were recorded with impedance cardiography. The method, FilterBCG, detects peaks in distal vibrations after filtering with individually tuned bandpass filters. In agreement with recent studies, we did not find peaks at AVO and AVC in limb vibrations directly. Interestingly, distal vibrations filtered with FilterBCG yielded reliable peaks at AVO (<inline-formula> <tex-math notation="LaTeX">$r^{2} =0.95$ </tex-math></inline-formula> A, 0.94 W, 0.77 K) and AVC (<inline-formula> <tex-math notation="LaTeX">$r^{2} =0.92$ </tex-math></inline-formula> A, 0.89 W, 0.68 K). FilterBCG measures AVO and AVC accurately from arm, wrist, and knee vibrations, and it outperforms the standard R-J interval method.
Uptake of DL-2-hydroxy-4-methylthio-butanoic acid (DL-HMB) in the broiler liver in vivo.

The methionine source DL-2-hydroxy-4methylthio-butanoic acid (DL-HMB; Alimet feed supplement) is widely used in the poultry industry. The purpose of this study was to determine the capacity of the broiler liver to remove DL-HMB from the circulation. Cannulae were implanted in the carotid artery and hepatic and hepatic portal veins in anesthetized male broilers (3.33 +/- 0.13 kg BW). In Experiment 1, birds (n = 5) were infused with DL-HMB solutions (diluted in saline, pH 7.2 to 7.4) into the hepatic portal vein at rates ranging from 4.4 to 22 mg/min per kg BW, whereas in Experiment 2, birds (n = 6) were infused with DL-HMB at rates ranging from 2.2 to 4.4 mg/min per kg BW. Plasma samples from each vessel were obtained before and after each 10-min DL-HMB infusion period with a 10-min clearance period allowed between each DL-HMB infusion. Regression analysis revealed a highly significant correlation in the amount of DL-HMB entering the liver via afferent vessels (afferent DL-HMB) and DL-HMB removed by the liver (y = 0.86(x) - 173, r2 = 0.98). The slope of this regression indicates that 86% of DL-HMB entering in afferent blood (i.e. from both the hepatic artery and hepatic portal vein) was removed or that the liver apparently metabolized 86% of the DL-HMB that entered the liver. The results indicate that the broiler liver has the capacity to remove DL-HMB from the circulation far in excess of that needed to metabolize DL-HMB that would enter the liver following gastrointestinal absorption in birds fed a conventional poultry diet. In addition, present results implicate the liver as a major site of removal from circulation and further metabolism of DL-HMB in chickens.
Semi-supervised Learning with GANs: Manifold Invariance with Improved Inference

Semi-supervised learning methods using Generative Adversarial Networks (GANs) have shown promising empirical success recently. Most of these methods use a shared discriminator/classifier which discriminates real examples from fake while also predicting the class label. Motivated by the ability of the GANs generator to capture the data manifold well, we propose to estimate the tangent space to the data manifold using GANs and employ it to inject invariances into the classifier. In the process, we propose enhancements over existing methods for learning the inverse mapping (i.e., the encoder) which greatly improves in terms of semantic similarity of the reconstructed sample with the input sample. We observe considerable empirical gains in semi-supervised learning over baselines, particularly in the cases when the number of labeled examples is low. We also provide insights into how fake examples influence the semi-supervised learning procedure.