Miracle-dz/UniFAR-FTUs huggingface dataset:
Epithelial hedgehog signals pattern the intestinal crypt-villus axis

Morphological development of the small intestinal mucosa involves the stepwise remodeling of a smooth-surfaced endodermal tube to form finger-like luminal projections (villi) and flask-shaped invaginations (crypts). These remodeling processes are orchestrated by instructive signals that pass bidirectionally between the epithelium and underlying mesenchyme. Sonic (Shh) and Indian (Ihh) hedgehog are expressed in the epithelium throughout these morphogenic events, and mice lacking either factor exhibit intestinal abnormalities. To examine the combined role of Shh and Ihh in intestinal morphogenesis, we generated transgenic mice expressing the pan-hedgehog inhibitor, Hhip (hedgehog interacting protein) in the epithelium. We demonstrate that hedgehog (Hh) signaling in the neonatal intestine is paracrine, from epithelium to Ptch1-expressing subepithelial myofibroblasts (ISEMFs) and smooth muscle cells (SMCs). Strong inhibition of this signal compromises epithelial remodeling and villus formation. Surprisingly, modest attenuation of Hh also perturbs villus patterning. Desmin-positive smooth muscle progenitors are expanded, and ISEMFs are mislocalized. This mesenchymal change secondarily affects the epithelium: Tcf4/β-catenin target gene activity is enhanced, proliferation is increased, and ectopic precrypt structures form on villus tips. Thus, through a combined Hh signal to underlying ISEMFs, the epithelium patterns the crypt-villus axis, ensuring the proper size and location of the emerging precrypt compartment.
Tap it again, Sam: Harmonizing Personal Environments towards Lifelong Learning

The increasing number of mobile vendors releasing NFC-enabled devices to the market and their prominent adoption has moved this technology from a niche product to a product with a large market-share. NFC facilitates natural interactions between digital world and physical learning environments. The scaffolding of learning ecologies is a key aspect for lifelong learners in their challenge to integrate learning activities into busy daily life. The contribution of this manuscript is twofold: first, a review of scientific literature in which NFC has been used with a direct or indirect purpose to learn is presented, and potential uses for learners are classified according to their type of interaction; based on these findings the NFC MediaPlayer is presented as an instantiation of an ecology of resources (EoR) in a lifelong learning context. Finally, shortcomings and best practices are highlighted in the conclusions, and future work is discussed.
Distinct Regulation of Adaxial-Abaxial Polarity in Anther Patterning in Rice[C][W][OA]

This study demonstrates that an RNA-dependent RNA polymerase involved in trans-acting small interfering RNA production plays a role in establishing adaxial-abaxial polarity in rice floral organs. A model is presented for anther patterning in rice. Establishment of adaxial-abaxial polarity is essential for lateral organ development. The mechanisms underlying the polarity establishment in the stamen remain unclear, whereas those in the leaf are well understood. Here, we investigated a rod-like lemma (rol) mutant of rice (Oryza sativa), in which the development of the stamen and lemma is severely compromised. We found that the rod-like structure of the lemma and disturbed anther patterning resulted from defects in the regulation of adaxial-abaxial polarity. Gene isolation indicated that the rol phenotype was caused by a weak mutation in SHOOTLESS2 (SHL2), which encodes an RNA-dependent RNA polymerase and functions in trans-acting small interfering RNA (ta-siRNA) production. Thus, ta-siRNA likely plays an important role in regulating the adaxial-abaxial polarity of floral organs in rice. Furthermore, we found that the spatial expression patterns of marker genes for adaxial-abaxial polarity are rearranged during anther development in the wild type. After this rearrangement, a newly formed polarity is likely to be established in a new developmental unit, the theca primordium. This idea is supported by observations of abnormal stamen development in the shl2-rol mutant. By contrast, the stamen filament is likely formed by abaxialization. Thus, a unique regulatory mechanism may be involved in regulating adaxial-abaxial polarity in stamen development.
Association of a basic 25K protein with membrane coating granules of human epidermis

Keratinocytes of the upper granular layers contain unique round-to-oval granules, 100-500 nm in diameter, in their peripheral cytoplasm. These granules (known as membrane coating granules [MCG], or lamellar granules) fuse with the apical cell surface of uppermost granular cells and discharge their contents into the intercellular space, where they are believed to play a role in establishing the permeability barrier of the epidermis and possibly in regulating the orderly desquamation of terminally differentiated keratinocytes. Using two monoclonal antibodies originally prepared against hair follicle antigens, we have identified a 25K epidermal protein in association with both MCG-like granules in the peripheral cytoplasm of granular cells as well as MCG- derived intercellular material. This protein is relatively basic (pI greater than 8), largely aqueous soluble, methionine deficient, and is relatively abundant in epidermis (comprising up to approximately 0.1% of soluble proteins). Its distribution is restricted to the granular layer of keratinized (cornified) stratified squamous epithelia. The identification of this protein component opens new avenues for studying the molecular mechanisms underlying the establishment of permeability barrier and/or regulation of desquamation.
Structural phase stability in nanocrystalline titanium to 161 GPa

Nanocrystalline titanium (nc-Ti) metal was investigated up to 161 GPa at room temperature using a diamond anvil cell. X-ray diffraction and electrical resistance techniques were used to investigate the compressibility and structural phase stability. nc-Ti is observed to undergo three structural phase transitions at high pressures, starting with &agr; → &ohgr; ? > at 10 GPa and followed by &ohgr; → &ggr; ? > at 127 GPa and &ggr; → &dgr; ? > at 140 GPa. The observed structural phase transitions, as well as compressibility, are consistent with previously reported values for coarse grained Ti (c-Ti). The high pressure experiments on nc-Ti samples do no show any significant variation of the &agr; → &ohgr; ? > transition pressure under varying non-hydrostatic conditions. This is in sharp contrast to c-Ti, where a significant decrease in the &agr; → &ohgr; ? > transition pressure is observed under increasing non-hydrostatic conditions. This would indicate that the decrease in grain size in nano grained titanium makes the &agr; → &ohgr; ? > phase transition less sensitive to shear stresses as compared to bulk or c-Ti.
Intracellular pH regulation in a nonmalignant and a derived malignant human breast cell line

Tumor cells in vivo often exist in an ischemic microenvironment that would compromise the growth of normal cells. To minimize intracellular acidification under these conditions, these cells are thought to upregulate H+ transport mechanisms and/or slow the rate at which metabolic processes generate intracellular protons. Proton extrusion has been compared under identical conditions in two closely related human breast cell lines: nonmalignant but immortalized HMT‐3522/S1 and malignant HMT‐3522/T4–2 cells derived from them. Only the latter were capable of tumor formation in host animals or long‐term growth in a low‐pH medium designed to mimic conditions in many solid tumors. However, detailed study of the dynamics of proton extrusion in the two cell lines revealed no significant differences. Thus, even though the ability to upregulate proton extrusion in a low pH environment (pHe) may be important for cell survival in a tumor, this ability is not acquired along with the capacity to form solid tumors and is not unique to the transformed cell. This conclusion was based on fluorescence measurements of intracellular pH (pHi) on cells that were plated on extracellular matrix, allowing them to remain adherent to proteins to which they had become attached 24 to 48 h earlier. Proton translocation under conditions of low pHe was observed by monitoring pHi after exposing cells to an acute acidification of the surrounding medium. Proton translocation at normal pHe was measured by monitoring the recovery after introduction of an intracellular proton load by treatment with ammonium chloride. Even in the presence of inhibitors of the three major mechanisms of proton translocation (sodium‐proton antiport, bicarbonate transport, and proton‐lactate symport) together with acidification of their medium, cells showed only about 0.4 units of reduction in pHi. This was attributed to a slowing of metabolic proton generation because the inhibitors were shown to be effective when the same cells were given an intracellular acidification. J. Cell. Physiol. 183:373–380, 2000. © 2000 Wiley‐Liss, Inc.
The SIMATIC Knowledge Manager

In this paper, we present details about the SIMATIC Knowledge Manager (SKM), a Textual CBR system that uses existing documents, such as FAQs and other useroriented documentation, and finds the most relevant documents for a given problem description. The major difference of the SKM compared to standard Information Retrieval tools and WWW search engines is that knowledge about the application domain can be brought into play when assessing the relevance of documents. Thus, not only the names of products, devices, and software components can be represented but also their relationships, such as dependencies between a series of products. Furthermore, the structure of the domain can be taken into account thus allowing a clustering of products into categories that express common properties. The SKM employs a case-based approach in that it considers the existing documents as cases and a user’s request as a query in the sense of the CBR paradigm. Also, by relying on these documents, a separate case authoring process is avoided which would require a substantial amount of both initial knowledge engineering when setting up the system as well as maintenance while the system is running.
Small-for-gestational age and large-for-gestational age thresholds to predict infants at risk of adverse delivery and neonatal outcomes: are current charts adequate? An observational study from the Born in Bradford cohort

Objectives Construct an ethnic-specific chart and compare the prediction of adverse outcomes using this chart with the clinically recommended UK-WHO and customised birth weight charts using cut-offs for small-for-gestational age (SGA: birth weight <10th centile) and large-for-gestational age (LGA: birth weight >90th centile). Design Prospective cohort study. Setting Born in Bradford (BiB) study, UK. Participants 3980 White British and 4448 Pakistani infants with complete data for gestational age, birth weight, ethnicity, maternal height, weight and parity. Main outcome measures Prevalence of SGA and LGA, using the three charts and indicators of diagnostic utility (sensitivity, specificity and area under the receiver operating characteristic (AUROC)) of these chart-specific cut-offs to predict delivery and neonatal outcomes and a composite outcome. Results In White British and Pakistani infants, the prevalence of SGA and LGA differed depending on the chart used. Increased risk of SGA was observed when using the UK-WHO and customised charts as opposed to the ethnic-specific chart, while the opposite was apparent when classifying LGA infants. However, the predictive utility of all three charts to identify adverse clinical outcomes was poor, with only the prediction of shoulder dystocia achieving an AUROC>0.62 on all three charts. Conclusions Despite being recommended in national clinical guidelines, the UK-WHO and customised birth weight charts perform poorly at identifying infants at risk of adverse neonatal outcomes. Being small or large may increase the risk of an adverse outcome; however, size alone is not sensitive or specific enough with current detection to be useful. However, a significant amount of missing data for some of the outcomes may have limited the power needed to determine true associations.
Automatically Correcting Bias in Speaker Recognition Systems

In this paper we present a general machine learning framework for score bias reduction and analysis in speaker recognition systems. The general principle is to learn a meta-system using recognition systems' errors, given the training and testing conditions in which they occurred. In the context of speaker recognition, the proposed method is able to reduce the bias introduced in scores due to a variety of factors such as channel mismatch, additive noise, gender mismatch, different speaking styles, etc. Moreover, this framework enables a deep understanding of the origins of score bias in any system, which will support an optimized system redesign. Preliminary results obtained with several state-of-the-art systems showed considerable improvement in original performance, in addition to identifying sources of system bias.
Estimating Microtubule Distributions from 2D Immunofluorescence Microscopy Images Reveals Differences among Human Cultured Cell Lines

Microtubules are filamentous structures that are involved in several important cellular processes, including cell division, cellular structure and mechanics, and intracellular transportation. Little is known about potential differences in microtubule distributions within and across cell lines. Here we describe a method to estimate information pertaining to 3D microtubule distributions from 2D fluorescence images. Our method allows for quantitative comparisons of microtubule distribution parameters (number of microtubules, mean length) between different cell lines. Among eleven cell lines compared, some showed differences that could be accounted for by differences in the total amount of tubulin per cell while others showed statistically significant differences in the balance between number and length of microtubules. We also observed that some cell lines that visually appear different in their microtubule distributions are quite similar when the model parameters are considered. The method is expected to be generally useful for comparing microtubule distributions between cell lines and for a given cell line after various perturbations. The results are also expected to enable analysis of the differences in gene expression underlying the observed differences in microtubule distributions among cell types.
Bacillus subtilis RecN binds and protects 3′-single-stranded DNA extensions in the presence of ATP

Bacillus subtilis RecN appears to be an early detector of breaks in double-stranded DNA. In vivo, RecN forms discrete nucleoid-associated structures and in vitro exhibits Mg2+-dependent single-stranded (ss) DNA binding and ssDNA-dependent ATPase activities. In the presence of ATP or ADP, RecN assembles to form large networks with ssDNA molecules (designated complexes CII and CIII) that involve ATP binding and requires a 3′-OH at the end of ssDNA molecule. Addition of dATP–RecA complexes dissociates RecN from these networks, but this is not observed following addition of an ssDNA binding protein. Apparently, ATP modulates the RecN–ssDNA complex for binding to ssDNA extensions and, in vivo, RecN–ATP bound to 3′-ssDNA might sequester ssDNA ends within complexes that protect the ssDNA while the RecA accessory proteins recruit RecA. With the association of RecA to ssDNA, RecN would dissociate from the DNA end facilitating the subsequent steps in DNA repair.
Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages

The male specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem-repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four populations of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of speciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze 9 common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two bonobo (Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of azoospermia candidates RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.
Unit selection speech synthesis using multiple speech units at non-adjacent segments for prosody and waveform generation

In this paper, we propose a speech synthesis method that combines a natural waveform concatenation based speech synthesis method and our baseline plural unit selection and fusion method. Two main features of the proposed method are (i) prosody regeneration from selected speech units and (ii) using multiple speech units at non-adjacent segments. The nonadjacent segments is the segment that the previous or following speech units in the optimum speech unit sequence are not adjacent in the database. By using the prosody of selected speech units, the original prosodic expressions and sounds of recorded speech are retained, while discontinuities are reduced by using multiple speech units at non-adjacent segments. MOS evaluations showed that the proposed method provides a clear improvement against the conventional unit selection method and our baseline method.
Phishing Detection using Content Based Associative Classification Data Mining

Phishing is a technique imitating an official websites of any company such as banks, institutes, etc. The purpose of phishing is that to theft a private and sensitive credentials of users such as password, username, PIN etc. Phishing detection is a technique to deal with this kind of malware activity. It is intended to prevent a phishing using data mining technique. MCAC Algorithm is gives higher efficiency towards to detect phishing activity. In MCAC algorithm does not consider a content based features of websites. It is intended to add content and page style features in that algorithm and change the system for better performance. This paper shows proposed method and flow chart. This paper also shows all the features of website which are considered during experimental analysis.
Resource-Aware Compiler Prefetching for Many-Cores

Super-scalar, out-of-order processors that can have tens of read and write requests in the execution window place significant demands on Memory Level Parallelism (MLP). Multi-and many-cores with shared parallel caches further increase MLP demand. Current cache hierarchies however have been unable to keep up with this trend, with modern designs allowing only 4-16 concurrent cache misses. This disconnect is exacerbated by recent highly parallel architectures (e.g. GPUs) where power and area per-core budget favor lighter cores with less resources. Support for hardware and software prefetch increase MLP pressure since these techniques overlap multiple memory requests with existing computation. In this paper, we propose and evaluate a novel Resource-Aware Prefetching (RAP) compiler algorithm that is aware of the number of simultaneous prefetches supported, and optimized for the same. We show that in situations where not enough resources are available to issue prefetch instructions for all references in a loop, it is more beneficial to decrease the prefetch distance and prefetch for as many references as possible, rather than use a fixed prefetched distance and skip prefetching for some references, as in current approaches. We implemented our algorithm in a GCC-derived compiler and evaluated its performance using an emerging fine-grained many-core architecture. Our results show that the RAP algorithm outperforms a well-known loop prefetching algorithm by up to 40.15% and the state-of-the art GCC implementation by up to 34.79%. Moreover, we compare the RAP algorithm with a simple hardware prefetching mechanism, and show improvements of up to 24.61%.
Removal of Hexavalent Chromium-Contaminated Wastewater by Micro-Emulsion Liquid Membrane Method

The micro-emulsion liquid membrane (MELM) was prepared for the extraction of hexavalent chromium (Cr (Ⅵ)) from wastewater. The membrane phase consists of kerosene as a membrane solvent, tributyl phosphate (TBP) as a mobile carrier, and sorbitan monooleate(Span80) as a surfactant. A NaOH solution is the internal aqueous phase. The effects of different conditions on the extractive of Cr (Ⅵ) were discussed. The results showed that the removal rate of Cr (Ⅵ) could reach 99.78% when the NaOH concentration was of 0.1mol•L-1 in internal phase, the pH values 1.0-1.75 in external phase, Rew of 1:3 and Roi of 2:1, stirring time of 12min and stirring rate of 320r•min-1, 10% of carrier and 15%-17% of surfactant.
Automated multi-objective control for self-adaptive software design

While software is becoming more complex everyday, the requirements on its behavior are not getting any easier to satisfy. An application should offer a certain quality of service, adapt to the current environmental conditions and withstand runtime variations that were simply unpredictable during the design phase. To tackle this complexity, control theory has been proposed as a technique for managing software's dynamic behavior, obviating the need for human intervention. Control-theoretical solutions, however, are either tailored for the specific application or do not handle the complexity of multiple interacting components and multiple goals. In this paper, we develop an automated control synthesis methodology that takes, as input, the configurable software components (or knobs) and the goals to be achieved. Our approach automatically constructs a control system that manages the specified knobs and guarantees the goals are met. These claims are backed up by experimental studies on three different software applications, where we show how the proposed automated approach handles the complexity of multiple knobs and objectives.