Miracle-dz/UniFAR-FTUs huggingface dataset:
Mom Knows Best: The Universality of Maternal Microbial Transmission

The sterile womb paradigm is an enduring premise in biology that human infants are born sterile. Recent studies suggest that infants incorporate an initial microbiome before birth and receive copious supplementation of maternal microbes through birth and breastfeeding. Moreover, evidence for microbial maternal transmission is increasingly widespread across animals. This collective knowledge compels a paradigm shift—one in which maternal transmission of microbes advances from a taxonomically specialized phenomenon to a universal one in animals. It also engenders fresh views on the assembly of the microbiome, its role in animal evolution, and applications to human health and disease.
A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius)

Background The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. Methodology DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738±68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. Conclusions For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts

Purpose We sought to identify the genetic defect in a four-generation Chinese family with autosomal dominant congenital lamellar cataracts and demonstrate the functional analysis with biosoftware of a candidate gene in the family. Methods Family history data were recorded. Clinical and ophthalmologic examinations were performed on family members. All the members were genotyped with microsatellite markers at loci considered to be associated with cataracts. Two-point LOD scores were calculated by using the Linkage Software after genotyping. A mutation was detected by using gene-specific primers in direct sequencing. Wild type and mutant proteins were analyzed with Online Bio-Software. Results Affected members of this family had lamellar cataracts. Linkage analysis was obtained at markers D3S2322 (LOD score [Z]=7.22, recombination fraction [θ]=0.0) and D3S1541 (Z=5.42, θ=0.0). Haplotype analysis indicated that the cataract gene was closely linked to these two markers. Sequencing the beaded filament structural protein 2 (BFSP2) gene revealed a G>A transversion in exon 5, which caused a conservative substitution of Arg to His at codon 339 (P.R339H). This mutation cosegregated with the disease phenotype in all affected individuals and was not observed in the unaffected family members or in 100 normal, unrelated individuals. Bioinformatic analyses showed that a highly conserved region was located around Arg339. Data generated with Online Bio-Software revealed that the mutation altered the protein’s hydrophobicity, hydrophobic moment, and chaperone and regulation activities. Conclusions This is the first reported case of a congenital lamellar cataract phenotype associated with the mutation of Arg339His (P.R339H) in BFSP2. It highlights the physiologic importance of the beaded filament protein and demonstrates a possible mechanism of action for the mutant gene.
HCCI Combustion Using Charge Stratification for Combustion Control

This work evaluates the effect of charge stratification on combustion phasing, rate of heat release and emissions for HCCI combustion. Engine experiments in both optical and traditional single cylinder engines were carried out with PRF50 as fuel. The amount of stratification as well as injection timing of the stratified charge was varied. It was found that a stratified charge can influence combustion phasing, increasing the stratification amount or late injection timing of the stratified charge leads to an advanced CA50 timing. The NOx emissions follows the CA50 advancement, advanced CA50 timing leads to higher NOx emissions. Correlation between CA50 can also be seen for HC and CO emissions when the injection timing was varied, late injection and thereby advanced CA50 timing leads to both lower HC and CO emissions. This trend can not be seen when the stratification amount was varied, increased stratification amount leads to higher CO emission and for operating condition with late CA50 timing the HC emissions also increase with increasing stratification amount. Optical studies, with high speed CCD camera, show that an increase in stratification leads to poor combustion quality near the cylinder walls, due to leaner mixtures near the cylinder walls and this results in higher HC and CO emissions. The maximum rate of heat release depends on stratification amount - a larger amount gives a lower rate of heat release but the main heat release is advanced. Varied injection timing results in different phasing of the main heat releases. The use of charge stratification for HCCI combustion can lead to a larger operating range, due to its effect on combustion phasing and rate of heat release, since the upper load range is partly restricted by too high rates of heat release leading to high pressure oscillations and the lower load to late combustion phasing leading to high cycle-to-cycle variations. Copyright © 2007 SAE International.
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal‐gas entropy correction?

The prediction of a ligand binding constant requires generating three‐dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine‐like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal‐gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root‐mean‐square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H‐bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1143–1149, 2002
Shape prior regularized continuous max-flow approach to image segmentation

In this work, we propose a novel segmentation method based on the continuous max-flow (CMF) formulation of the Potts model incorporating the statistical shape model. We increase the robustness and accuracy of the Potts model by using the prior shape knowledge from the Principal Component Analysis (PCA) to represent the desired shape. Our multi-label model can segment several objects simultaneously and guarantee one label with the structure similar to the shape prior. The proposed approach is applied to both synthetic and medical image of liver from computed tomography (CT). Numerous numerical experiments demonstrate that our model is efficient and with good quality in practice.
A Search and Retrieval Framework for the management of copyrighted audiovisual content

This paper presents a search and retrieval framework that enables the management of intellectual property in the World Wide Web. This twofold framework helps users to detect digital rights infringements of their copyrighted content. In order to detect possible copyright infringments, first the system crawls the Web to search replicas of usertpsilas images, and later evaluates if the copies have been taken respecting the terms stated by the owner. On the other hand, this framework also helps users in finding something interesting in the Web. It will provide copyrighted content to users according to their preferences and to intellectual property rights integrating search and retrieval with digital rights management tools.
Scapular Tip Free Flap for Head and Neck Reconstruction

Objectives Head and neck reconstruction is still challenging in terms of esthetic and functional outcomes. This study investigated the feasibility of the angular branch-based scapular tip free flap (STFF). Methods This was a retrospective study of 17 patients undergoing maxillectomy and mandibulectomy and either primary or secondary reconstruction by STFF. This study included surgical, esthetic, and functional outcomes, and detailed data are presented regarding the flap, such as pedicle length, size of the harvested bone, and failure rate. Medical photographs were used to estimate the esthetic outcome, and computed tomography was used to check the flap status postoperatively. Results The data were collected from April 2013 to April 2014. Eight patients underwent maxillary reconstruction, and nine underwent mandibular reconstruction. Maxillary defects usually included unilateral alveolar structures and the palate; mandibular defects were usually those involving mandibular angle and short segment. Vein grafting was not required in any of the patients. Flap failure occurred in one of the 17 patients (5.9%) with successful reconstruction after revision. Of the eight maxillectomy patients, orbital revisions for diplopia after maxillary reconstruction were performed in two patients (25%), and oroantral fistula repair was performed in one patient (12.5%). Conclusion This study demonstrated the reconstructive advantages of the angular branch-based STFF, long pedicle, low flap failure, 3-dimensional nature of bone and soft tissues (chimeric flap), and small rate of donor site morbidity with free ambulation. This flap is an excellent option for use in complex three-dimensional head and neck reconstruction.
New Insight on the Influence of Chemistry on Nucleation and Growth in High Temperature Superconducting Wires Through Spectrum Imaging

One successful approach for the manufacture of rare-earth cuprate superconductor (REBCO) wires is based on a post-deposition ex situ conversion of metal-organic deposited (MOD) precursors on textured substrate templates. [1,2] In the conversion step, the precursor crystallizes to the superconducting phase with initial nucleation at the template followed by homoepitaxial growth through the thickness of the coating. The deposition of multiple coatings is often used to achieve thicker conductor layers that can carry more current. However, a chemically segregated layer – referred to as the “interlayer” - invariably forms at the interface between coatings in these multi-coat films. This chemically-segregated interlayer disrupts the propagation of the growth front and causes a loss of texture quality in the succeeding layer. [3] In this work using electron beam imaging and elemental mapping, we identified a mechanism by which the REBCO grows past the interlayer in two-layer films that also provides an explanation for degraded texture above the interlayer. In to study the conversion and growth process, double-layer precursor films were quenched at various points in the process, and the converted films were examined in cross-section by SEM Cross-sections for TEM and SEM produced by the the the the
Remote Thin-Client Access to Spatial Database Systems

Numerous federal agencies produce official statistics that are made accessible to ordinary citizens for searching and data retrieval. This is often done via the Internet through a web browser interface. If this data is presented in textual format, it can often be searched and retrieved by such attributes as topic, responsible agency, keywords, or press release. However, if the data is of spatial nature, e.g., in the form of a map, then using text-based queries is often too cumbersome for the intended audience. We propose to use the capabilities of the SAND Spatial Browser to provide more power to users of these databases. Using the SAND Spatial Browser allows users to define the spatial region of interest with greater specificity, instead of forcing them to retrieve data just for a particular location or a region with a predefined boundary. They can also make use of ranking which is the ability to retrieve data in the order of distance from other instances of the data or aggregates of data that are user-defined. Work is distributed between the SAND server and the individual clients for query evaluation, data visualization and data management. This enables the minimization of the necessary requirements for system resources on the client side while maximizing the number of connections one server can handle concurrently. Concrete experience with interfacing the SAND system with FedStats data is also discussed.
Kolmogorov's law for two-dimensional electron-magnetohydrodynamic turbulence

The analogue of the Kolmogorov's four-fifths law is derived for two-dimensional, homogeneous, isotropic EMHD turbulence in the energy cascade inertial range. Direct numerical simulations for the freely decaying case show that this relation holds true for different values of the adimensional electron inertial length scale, de. The energy spectrum is found to be close to the expected Kolmogorov spectrum.
A Collaborative Initiative For the Containment of Antimicrobial Resistance in Mexico

Antimicrobial resistance exacts worldwide an increasingly significant clinical and economic toll. Despite the international calls for urgent action, antimicrobial use and resistance have been low on the Mexican government's policy agenda. In early 2010, a multidisciplinary group of experts launched a national initiative for containment of antimicrobial resistance that was endorsed by major medical, veterinary and public health institutions. The initiative called for seven priority actions including the creation of an ad hoc intersectoral advisory group, a requirement that human and veterinary antibiotics be dispensed only with prescription, and the establishment of effective surveillance systems. A consensus document was disseminated among key decision‐makers at the ministries of Health and Agriculture and the legislature. The Ministry of Health (MoH) enacted a decree effective as of August 2010, which enforced the regulations that required medical prescriptions for the sale of human antibiotics. While the information disseminated by the MoH did focus on the dangers of self‐medication, it failed to highlight the inherent perils of antibiotic resistance or the consequences of antibiotic use in food‐animals. Following the decree, there was a surge of medical offices controlled by retail pharmacies. In the veterinary sector, voluntary guidelines were developed for good husbandry practices, including antibiotic use in food animals; five antimicrobials for use in food‐animals were banned. No intersectoral advisory group or surveillance systems were established. This study describes a bottom‐top approach in Mexico for the development of a national strategy to improve antibiotic use and contain antimicrobial resistance. Its experiences suggest that, in countries such as Mexico that lack strong regulatory systems and surveillance capacities, a more systemic approach is warranted. Future efforts should begin with early involvement of key stakeholders and informing policy makers, professionals and the population at large about the critical importance of antibiotic resistance.
Specialty Fibers for Terahertz Generation and Transmission: A Review

Terahertz (THz) frequency range, lying between the optical and microwave frequency ranges covers a significant portion of the electro-magnetic spectrum. Though its initial usage started in the 1960s, active research in the THz field started only in the 1990s by researchers from both optics and microwaves disciplines. The use of optical fibers for THz application has attracted considerable attention in recent years. In this paper, we review the progress and current status of optical fiber-based techniques for THz generation and transmission. The first part of this review focuses on THz sources. After a review on various types of THz sources, we discuss how specialty optical fibers can be used for THz generation. The second part of this review focuses on the guided wave propagation of THz waves for their transmission. After discussing various wave guiding schemes, we consider new fiber designs for THz transmission.
A SUSTAINABLE WORLD – THE LOCAL IN TERMS OF THE GLOBAL : AN ECOLOGICAL FOOTPRINT ANALYSIS PERSPECTIVE

This paper considers, by way of literature review and analysis, how Ecological Footprint Analysis (Footprint-Analysis) can be applied to assess the consequences of local behaviour in terms of its contribution to, or detraction from, the goal of humanity living sustainably at the global level (that is, for there to be a sustainable-world). The South Australian setting is used as a case study against which the theoretical findings are applied, and shows that South Australia's citizens are, in Footprint-Analysis terms, detracting from a global sustainable-world goal. The South Australian Government's Ecological-Footprint reduction target, although having 40-years for its achievement, will not remedy this problem.
High quality text-to-speech synthesis: a comparison of four candidate algorithms

We investigate the use of four candidate speech models in the context of high quality text-to-speech systems (HQ-TTS), address problems typically encountered by their prosody matching and segment concatenation modules, and compare their performances regarding: the segment database compression ratio they allow, the computational load of the related synthesis algorithms, as well as their intelligibility and subjective segmental quality. The models addressed are: the classical auto-regressive (LPC) one, the hybrid harmonic/stochastic (H/S) model proposed by Griffin and Lim (1988) and by Abrantes, Marques and Transcoso (1991), the 'null' model, as implemented by the time-domain pitch-synchronous overlap-add (TD-PSOLA) synthesis algorithm, and the multi-band re-synthesis pitch-synchronous overlap-add (MBR-PSOLA) model. <<ETX>>
A Note on Perfect Matchings in Uniform Hypergraphs

We determine the exact minimum $\ell$-degree threshold for perfect matchings in $k$-uniform hypergraphs when the corresponding threshold for perfect fractional matchings is significantly less than $\frac{1}{2}\left( \begin{array}{c} n \\ k- \ell\end{array}\right)$. This extends our previous results that determine the minimum $\ell$-degree thresholds for perfect matchings in $k$-uniform hypergraphs for all $\ell\ge k/2$ and provides two new (exact) thresholds: $(k,\ell)=(5,2)$ and $(7,3)$.
QX-type infectious bronchitis virus in commercial flocks in the UK

THE QX infectious bronchitis virus (IBV) strain was described for the first time in China in 1996 ([Wang and others 1998][1]) as the cause of proventriculitis in chickens. Since then, several QX-type strains have been identified in China, but most cases of the infection were associated with renal
Brain connectivity in pathological and pharmacological coma

Higher-order areas encompassing lateral and midline frontoparietal networks show no activation in either volunteers under deep anesthesia or in patients in a “vegetative state. ” At the opposite, patients in minimally conscious state can show activation of the higher-order areas sometimes similar to healthy control subjects (Laureys, 2005). A common finding of studies on both pathological and pharmacological coma is an impairment in the activity of a widespread cortical network, encompassing bilateral frontoparietal associative cortices, but not of “lower level” sensory cortices (Baars et al., 2003; Alkire and Miller, 2005; Laureys, 2005). As we will see, a decrease in regional activation seems not sufficient to loose awareness but also requires a functional disconnection within that network and with the thalami, in line with a number of current theoretical views on consciousness (Tononi, 2004; Dehaene et al., 2006; Seth et al., 2006).
Effect of Drying Phase on the Agglomerates Prepared by Spherical Crystallization

In this paper, differences in porosity, compressive strength and tablet- forming ability of carbamazepine crystals agglomerated under similar condition, but subjected to different drying temperatures are reported. The agglomerates were prepared by spherical crystallization method and thereafter dried without agitation at different temperature. An increased drying temperature did not affect the shape and structure texture of dried particles and did not cause them to fracture. Drying of particles at higher temperature suppressed the particle contraction as a consequence of fast evaporation and hence produced particles of larger mean diameter, higher porosity and thus lower compressive strength than those dried at lower temperature. Through a relationship with particle porosity, the drying rate also affected the ability of particles to form tablets.
Integrated self-supplied system for environmental temperature sensing

In this paper we present a 4-mm2 battery-less temperature sensor, designed to collect and periodically transmit information to an ambient monitoring system. It consists of a 0.35-µm BCD SOI technology based chip including an ultra-low power integrated circuit and an energy harvesting supply unit made by 34 series-parallel connected photovoltaic cells. Each cell consists of a trench insulated p-n junction. Series connections among cells are possible because of the lack, guaranteed by the SOI insulation, of the substrate parasitic diode, typical in standard CMOS technology. The system is fully compliant with real-time applications and can work in low illumination conditions and with large variations of the photovoltaic voltage.