Miracle-dz/UniFAR-FTUs huggingface dataset:
Preconception Prebiotic and Sitagliptin Treatment in Obese Rats Affects Pregnancy Outcomes and Offspring Microbiota, Adiposity, and Glycemia

Maternal obesity is associated with increased risk of pregnancy complications and greater risk of obesity in offspring, but studies designed to examine preconception weight loss are limited. The objective of this study was to determine if a combined dietary [oligofructose (OFS)] and pharmacological (sitagliptin) preconception intervention could mitigate poor pregnancy outcomes associated with maternal obesity and improve offspring metabolic health and gut microbiota composition. Diet-induced obese female Sprague-Dawley rats were randomized to one of four intervention groups for 8 weeks: (1) Obese-Control (consumed control diet during intervention); (2) Obese-OFS (10% OFS diet); (3) Obese-S (sitagliptin drug); (4) Obese-OFS + S (combination treatment). Two reference groups were also included: (5) Obese-HFS (untreated obese consumed high fat/sucrose diet throughout study); (6) Lean-Control (lean reference group that were never obese and consumed control diet throughout). Offspring consumed control diet until 11 weeks of age followed by HFS diet until 17 weeks of age. The Obese-OFS + S rats lost weight during the intervention phase whereas the OFS and S treatments attenuated weight gain compared with Obese-HFS (p < 0.05). Gestational weight gain was lowest in Obese-OFS + S rats and highest in Obese-HFS rats (p < 0.05). Prepregnancy intervention did not affect reproductive parameters but did affect pregnancy outcomes including litter size. Male Obese-OFS offspring had significantly lower percent body fat than Obese-HFS at 17 weeks. Female Obese-S and Obese-OFS offspring had significantly lower fasting glucose at 17 weeks compared with Obese-Control and Obese-HFS. Clostridium cluster XI was higher in Obese-HFS and Obese-S dams at birth compared with all other groups. Dams with an adverse pregnancy outcome had significantly lower (p = 0.035) Lactobacillus spp. compared with dams with normal or small litters. At weaning, male offspring of Obese-HFS had higher levels of Methanobrevibacter than all other groups except Obese-S and female Obese-HFS offspring had higher Enterobacteriaceae compared with all other groups. At 11 and 17 weeks of age, Bacteroides/Prevotella spp. was significantly lower in male and female offspring of Obese-HFS dams compared with all other groups except Obese-OFS + S. Modest weight loss induced with a diet-drug combination did not affect maternal fecundity but did have sex-specific effects on offspring adiposity and glycemia that may be linked to changes in offspring microbiota.
Network formation games for the link selection of cooperative localization in wireless networks

Recently, localization has become an indispensable technique for wireless applications. In view of the limitation of global position system (GPS) in certain environments, alternative approaches are in demand. In this paper, we consider a cooperative localization approach named sum-product algorithm over a wireless network (SPAWN). Although SPAWN theoretically facilitates cooperative localization, it has several practical limitations. Specifically, SPAWN results in high computational complexity and increased network traffic. The main complexity of SPAWN lies in the selection of agents/anchors involved in the cooperative localization. To this end, we formulate the agent/anchor selection problem into a network formation game. Together with a practical limit on the number of agents/anchors used for cooperative localization, our proposed approach can markedly reduce the computational complexity and the resultant network traffic. Simulations show that these advantages come with a slight degradation in the localization mean squared error (MSE) performance.
Fast multi-frame motion estimation for video processing

Motion estimation is being utilized more and more in video post-production and display for a wide range of applications. These applications require accurate motion trajectories at low computational cost. This paper presents a novel motion estimation algorithm that combines the accuracy of MAP estimation with the speed of hierarchical block-matching algorithm (BMA). This MAP estimation uses three consecutive pictures, instead of the conventional two, and one previously estimated motion field to exploit the temporal correlation between motion fields and to determine motion in occluded areas. The optimization of the MAP estimation is performed using full search and implemented by means of look-up tables. The full search ensures that the optimization converges to the global minimum, while the look-up tables dramatically reduce the computational cost. Experiment results show that the proposed algorithm provides motion trajectories that are much more accurate than those obtained using the full-search BMA and hierarchical BMA. It is much faster than the full-search BMA, but slower than the hierarchical BMA.
Pros and cons: cryo‐electron microscopic evaluation of block faces versus cryo‐sections from frozen‐hydrated skin specimens prepared by different techniques

Over the last two decades, several different preparative techniques have been developed to investigate frozen‐hydrated biological samples by electron microscopy. In this article, we describe an alternative approach that allows either ultrastructural investigations of frozen human skin at a resolution better than 15 nm or sample throughput that is sufficiently high enough for quantitative morphological analysis. The specimen preparation method we describe is fast, reproducible, does not require much user experience or elaborate equipment. We compare high‐pressure freezing with plunge freezing, and block faces with frozen‐hydrated slices (sections), to study variations in cell thickness upon hydration changes. Plunge freezing is optimal for morphological and stereological investigations of structures with low water content. By contrast, high‐pressure freezing proved optimal for high‐resolution studies and provided the best ultrastructural preservation. A combination of these fast‐freezing techniques with cryo‐ultramicrotomy yielded well‐preserved block faces of the original biological material. Here we show that these block faces did not exhibit any of the artefacts normally associated with cryo‐sections, and – after evaporating a heavy metal and carbon onto the surface – are stable enough in the electron beam to provide high‐resolution images of large surface areas for statistical analysis in a cryo‐SEM (scanning electron microscope). Because the individual preparation steps use only standard equipment and do not require much experience from the experimenter, they are generally more usable, making this approach an interesting alternative to other methods for the ultrastructural investigation of frozen‐hydrated material.
Designing Rectangular Slot Loop Antenna for WLAN Application

This paper presents the design of rectangular microstrip slot loop antenna that competently achieves dual frequency operation by using a microstrip feed line. This antenna is designed at the resonance frequency 2.4 GHz and 5.2 GHz thereby covering the required frequency-bandwidth of 2.4- 2.4836 GHz and 5.15-5.35 GHz, which are widely used in Wireless LAN (WLAN). The characteristics of antennas are proposed and analyzed for instance input impedance, S11 parameter and far field radiation patterns. The antenna is analyzed by finite difference time domain (FDTD) method which can predict and analysis of the electromagnetic responses of complex problems.
Comparison of three techniques for isolation of Rhodococcus (Corynebacterium) equi from contaminated sources

Inoculation of a liquid medium comprised of Trypticase soy broth (BBL Microbiology Systems), cycloheximide, nalidixic acid, penicillin, and potassium tellurite and subcultured onto M3 medium plus potassium tellurite was highly successful for the isolation of Rhodococcus (Corynebacterium) equi from soil.
Thyroid peroxidase antibodies in pregnant women with type 1 diabetes: Impact on thyroid function, metabolic control and pregnancy outcome

Objective. In pregnant women with type 1 diabetes, we evaluated whether the presence of thyroid peroxidase autoantibodies (anti‐TPO) was associated with changes in thyroid function, metabolic control and pregnancy outcome. Design/setting. Prospective study, Denmark. Population. Ninety‐six consecutive pregnant women with type 1 diabetes. Twenty‐five healthy pregnant controls. Methods. At 8, 14, 21, 27 and 33 weeks, the diabetic women self‐monitored plasma glucose (SMPG) (8/day) for 3 days and had blood samplings obtained. Main outcome measures. Thyroid‐stimulating hormone (TSH), free thyroxin (T4), hemoglobin A1C (HbA1C), anti‐TPO, pregnancy outcome. Results. Anti‐TPO was detected in 31 (32%) of the pregnant diabetic women compared with two women (8%) in the healthy controls (p = 0.015). The presence of anti‐TPO was associated with higher TSH at 8 (p <0.0001) and 14 weeks (p <0.05) and lower free T4 at 8 weeks (p <0.05) compared with anti‐TPO negative women. Twenty untreated anti‐TPO positive women had higher TSH compared with untreated, anti‐TPO negative women (p <0.05), but comparable free T4. At inclusion, 25% had TSH above the recommended treatment goal for levothyroxine (TSH>2.5 mIU/l), most prevalently among anti‐TPO positive women. Sixteen women (17%) were treated for thyroid disorder during pregnancy. No differences were detected between the diabetic women with and without anti‐TPO regarding HbA1C, insulin dose, median SMPG or pregnancy outcome. Conclusions. Anti‐TPO was present in one‐third of pregnant women with type 1 diabetes and associated with slightly higher TSH, but not poorer glycemic control or adverse birth outcome. A total of 17% of women with type 1 diabetes were treated for thyroid disorder during pregnancy.
Lean laboratories: laboratory medicine needs to learn from other industries how to deliver more for less

Laboratory medicine faces unprecedented challenges worldwide. Demand continues to grow year on year both in volume and complexity as populations age and healthcare becomes ever more sophisticated. Crude test numbers are rising at between 6% and 10% per annum1 and revenue continues to fall, at least in relative terms, irrespective of the type of funding system. In the UK, the Department of Health is looking to an absolute cut in annual pathology costs of 20%. 2 In Australia, the federal government has capped growth in the pathology budget at 5% per annum for the next 5 years, closely linked with a variety of strategies effectively focusing on demand management. The equivalent move in the USA is a cut in the clinical laboratory fee schedule for Medicare of 1.75% year on year until 2015, capped off by an additional 2% cut enacted by Congress in February 2012. With a stagnant general economy, patients benefiting from employer based health schemes are expected to meet an increasing percentage of their health costs and this is leading to an escalating bad debt problem for commercial pathology in the USA. Falling revenue needs to be set against a background of rising overheads, not simply in terms of consumable costs and maintenance but due to the increasing diversion of resources to manage regulatory compliance and an upward trend in litigation. In the USA, federal and state clinical laboratory regulators are tightening enforcement of the demands of the Clinical Laboratory Improvement Act well beyond the hospital environment. In the UK, Clinical Pathology Accreditation and peer review processes are now complicated by the introduction of the Care Quality Commission. And there is a global trend towards the use of the more demanding ISO 15189 as a benchmark for competence. In North America, traditionally in the vanguard of medicolegal …
Improving structure alignment-based prediction of SCOP families using Vorolign Kernels

MOTIVATION The slow growth of expert-curated databases compared to experimental databases makes it necessary to build upon highly accurate automated processing pipelines to make the most of the data until curation becomes available. We address this problem in the context of protein structures and their classification into structural and functional classes, more specifically, the structural classification of proteins (SCOP). Structural alignment methods like Vorolign already provide good classification results, but effectively work in a 1-Nearest Neighbor mode. Model-based (in contrast to instance-based) approaches so far have been shown to be of limited values due to small classes arising in such classification schemes. RESULTS In this article, we describe how kernels defined in terms of Vorolign scores can be used in SVM learning, and explore variants of combined instance-based and model-based learning, up to exclusively model-based learning. Our results suggest that kernels based on Vorolign scores are effective and that model-based learning can yield highly competitive classification results for the prediction of SCOP families. AVAILABILITY The code is made available at: http://wwwkramer.in. tum.de/research/applications/vorolign-kernel.
Thermal relics: Do we know their abundances?

The relic abundance of a particle species that was once in thermal equilibrium in the expanding Universe depends upon a competition between the annihilation rate of the species and the expansion rate of the Universe. Assuming that the Universe is radiation dominated at early times the relic abundance is easy to compute and well known. At times earlier than about 1 sec after the bang there is little or no evidence that the Universe had to be radiation dominated, although that is the simplest–and standard–assumption. Because early-Universe relics are of such importance both to particle physics and to cosmology, we consider in detail three nonstandard possibilities for the Universe at the time a species’ abundance froze in: energy density dominated by shear (i.e., anisotropic expansion), energy density dominated by some other nonrelativistic species, and energy density dominated by the kinetic energy of the scalar field that sets the gravitational constant in a Brans-Dicke-Jordan cosmological model. In the second case the relic abundance is less than the standard value, while in the other two cases it can be enhanced by a significant factor. We also mention two other more exotic possibilities for enhancing the relic abundance of a species–a larger value of Newton’s constant at early times (e.g., as might occur in superstring or Kaluza-Klein theories) or a component of the energy density at early times with a very stiff equation of state (p>ρ/3), e.g., a scalar field φ with potential V(φ)=β‖φ‖n with n>4. Our results have implications for dark-matter searches and searches for particle relics in general.
Evolution in Finitely Repeated Coordination Games

I apply a version of Kandori et al. (1993, Econometrica, 61, 29–56) and Young's (1993, Econometrica, 61, 57–84) evolutionary dynamic to finitely repeated coordination games. The dynamic is modified by allowing mutations to affect only off path beliefs. I find that repetition within a match leads agents to sacrifice current payoffs in order to increase payoffs in later stages. As a consequence, evolution leads to (almost) efficiency.
Seasonal gene expression in a migratory songbird

The annual migration of a bird can involve thousands of kilometres of nonstop flight, requiring accurately timed seasonal changes in physiology and behaviour. Understanding the molecular mechanisms controlling this endogenous programme can provide functional and evolutionary insights into the circannual biological clock and the potential of migratory species to adapt to changing environments. Under naturally timed photoperiod conditions, we maintained captive Swainson's thrushes (Catharus ustulatus) and performed RNA sequencing (RNA‐Seq) of the ventral hypothalamus and optic chiasma to evaluate transcriptome‐wide gene expression changes of individuals in migratory condition. We found that 188 genes were differentially expressed in relation to migratory state, 86% of which have not been previously linked to avian migration. Focal hub genes were identified that are candidate variables responsible for the occurrence of migration (e.g. CRABP1). Numerous genes involved in cell adhesion, proliferation and motility were differentially expressed (including RHOJ, PAK1 and TLN1), suggesting that migration‐related changes are regulated by seasonal neural plasticity.
Optimization and troubleshooting in PCR.

The use of polymerase chain reaction (PCR) to generate large amounts of a desired product can be a double-edged sword. Failure to amplify under optimum conditions can lead to the generation of multiple undefined and unwanted products, even to the exclusion of the desired product. At the other extreme, no product may be produced. A typical response at this point is to vary one or more of the many parameters that are known to contribute to primer-template fidelity and primer extension. High on the list of optimization variables are Mg concentrations, buffer pH, and cycling conditions. With regard to the last, the annealing temperature is most important. The situation is further complicated by the fact that some of the variables are quite interdependent. For example, because dNTPs directly chelate a proportional number of Mg ions, an increase in the concentration of dNTPs decreases the concentration of free Mg available to influence polymerase function. This article discusses various optimization strategies, including touchdown PCR and hot-start PCR.
Functional Analysis of Four Bile Salt Hydrolase and Penicillin Acylase Family Members in Lactobacillus plantarum WCFS1

ABSTRACT Bile salts play an important role in the digestion of lipids in vertebrates and are synthesized and conjugated to either glycine or taurine in the liver. Following secretion of bile salts into the small intestine, intestinal microbes are capable of deconjugating the glycine or taurine from the bile salts, using an enzyme called bile salt hydrolase (Bsh). Intestinal lactobacilli are regarded as major contributors to bile salt hydrolysis in vivo. Since the bile salt-hydrolyzing strain Lactobacillus plantarum WCFS1 was predicted to carry four bsh genes (bsh1, bsh2, bsh3, and bsh4), the functionality of these bsh genes was explored using Lactococcus lactis heterologous overexpression and multiple bsh deletion strains. Thus, Bsh1 was shown to be responsible for the majority of Bsh activity in L. plantarum WCFS1. In addition, bsh1 of L. plantarum WCFS1 was shown to be involved in conferring tolerance to specific bile salts (i.e., glycocholic acid). Northern blot analysis established that bsh1, bsh2, bsh3, and bsh4 are all expressed in L. plantarum WCFS1 during the exponential growth phase. Following biodiversity analysis, bsh1 appeared to be the only bsh homologue that was variable among L. plantarum strains; furthermore, the presence of bsh1 correlated with the presence of Bsh activity, suggesting that Bsh1 is commonly responsible for Bsh activity in L. plantarum strains. The fact that bsh2, bsh3, and bsh4 genes appeared to be conserved among L. plantarum strains suggests an important role of these genes in the physiology and lifestyle of the species L. plantarum. Analysis of these additional bsh-like genes in L. plantarum WCFS1 suggests that they might encode penicillin acylase rather than Bsh activity, indicating their implication in the conversion of substrates other than bile acids in the natural habitat.
Superfluous Transgene Integration in Plants

Referee: Dr. Paul Hooykass, Institut of Molecular Plant Sciences, Leiden University, Clusius Laboratory, Wassenaarseweg 64, 2333, Al Leiden, Netherlands Recent reports suggest the transfer of superfluous DNA sequences to plant genomes during transformation processes. This review investigates the evidence from the published literature for the prevalence of this phenomenon and highlights methods to limit or prevent DNA transfer and subsequent potentially detrimental evolutionary consequences. Evidence for superfluous foreign DNA transfer using both Agrobacterium-mediated transformation and direct DNA transfer methods such as microprojectile bombardment and PEG-mediated transformation of protoplasts is reported. In the case of Agrobacterium-mediated transformation, the lack of information on the integration of sequences from outside of the T-DNA borders has been due to the general belief by researchers that T-DNA processing is precise. This assumption was based on analysis of T-DNA in tumors and as a result the majority of T-DNA integration events have been identified exclusively using DNA probes, which are homologous only to DNA from within the T-DNA borders. Where direct gene transfer protocols are employed, any part of the transforming plasmid and indeed accompanying carrier DNA may become integrated into the plant genome. The main body of evidence proving that superfluous vector DNA sequences are present in plant genomes transformed using direct transfer methods is confined to the identification of plasmid concatamers integrated into plant genomes. The limited amount of recorded evidence pertaining to superfluous vector DNA integration in transgenic plants and transformed tissues makes it impossible to draw definitive conclusions as to the factors involved in promoting this phenomenon. However, there are methods available for removing superfluous sequences from transgenic plants. These have been developed for the removal of selectable marker genes, whose presence in transgenic plants has been a source of much controversy, but can equally be applied to other DNA sequences. Suggestions have been made in the review that might limit or prevent the integration of superfluous vector sequences during transformation procedures; however, these are not proven and further research is required.
catena-Poly[[[diaquacopper(II)]-bis[μ-1,5-bis(1H-imidazol-1-yl)pentane-κ2 N 3:N 3′]] naphthalene-1,5-disulfonate]

In the title complex, {[Cu(C11H16N4)2(H2O)2](C10H6O6S2)}n, the CuII atom, lying on an inversion center, is six-coordinated by two water molecules and four N atoms from four 1,5-bis(1H-imidazol-1-yl)pentane (biim-5) ligands in a distorted octahedral geometry. Adjacent CuII atoms are linked by two biim-5 ligands, forming a chain along [111]. Two atoms of the pentane group are disordered over two sets of sites, with an occupancy ratio of 0.554 (18):0.446 (18). Intermolecular O—H⋯O hydrogen bonds link the chains and the centrosymmetric naphthalene-1,5-disulfonate anions into a layer structure parallel to (0-11).
A Geometric Approach to Archetypal Analysis and Nonnegative Matrix Factorization

ABSTRACT Archetypal analysis and nonnegative matrix factorization (NMF) are staples in a statistician's toolbox for dimension reduction and exploratory data analysis. We describe a geometric approach to both NMF and archetypal analysis by interpreting both problems as finding extreme points of the data cloud. We also develop and analyze an efficient approach to finding extreme points in high dimensions. For modern massive datasets that are too large to fit on a single machine and must be stored in a distributed setting, our approach makes only a small number of passes over the data. In fact, it is possible to obtain the NMF or perform archetypal analysis with just two passes over the data.