Miracle-dz/UniFAR-FTUs huggingface dataset:
Priming the Surface of Orthopedic Implants for Osteoblast Attachment in Bone Tissue Engineering

The development of better orthopedic implants is incessant. While current implants can function reliably in the human body for a long period of time, there are still a significant number of cases for which the implants can fail prematurely due to poor osseointegration of the implant with native bone. Increasingly, it is recognized that it is extremely important to facilitate the attachment of osteoblasts on the implant so that a proper foundation of extracellular matrix (ECM) can be laid down for the growth of new bone tissue. In order to facilitate the osseointegration of the implant, both the physical nanotopography and chemical functionalization of the implant surface have to be optimized. In this short review, however, we explore how simple chemistry procedures can be used to functionalize the surfaces of three major classes of orthopedic implants, i.e. ceramics, metals, and polymers, so that the attachment of osteoblasts on implants can be facilitated in order to promote implant osseointegration.
A highly conserved retinoic acid responsive element controls wt1a expression in the zebrafish pronephros

The Wilms' tumor suppressor gene Wt1 encodes a zinc-finger transcription factor that plays an essential role in organ development, most notably of the kidney. Despite its importance for organogenesis, knowledge of the regulation of Wt1 expression is scarce. Here, we have used transgenesis in zebrafish harboring two wt1 genes, wt1a and wt1b, in order to define regulatory elements that drive wt1 expression in the kidney. Stable transgenic lines with approximately 30 kb of the upstream genomic regions of wt1a or wt1b almost exactly recapitulated endogenous expression of the wt1 paralogs. In the case of wt1b, we have identified an enhancer that is located in the far upstream region that is necessary and sufficient for reporter gene expression in the pronephric glomeruli. Regarding wt1a, we could also identify an enhancer that is located approximately 4 kb upstream of the transcriptional start site that is required for expression in the intermediate mesoderm. Interestingly, this intermediate mesoderm enhancer is highly conserved between fish and mammals, is bound by members of the retinoic acid receptor family of transcription factors in gel shift experiments and mediates responsiveness to retinoic acid both in vivo and in cell culture. To our knowledge, this is the first functional demonstration of defined regulatory elements controlling Wt1 expression in vivo. The identification of kidney-specific enhancer elements will help us to better understand the integration of extracellular signals into intracellular networks in nephrogenesis.
Machine Translation Systems for WMT 2017

This paper describes the Johns Hopkins University submissions to the shared translation task of EMNLP 2017 Second Conference on Machine Translation (WMT 2017). We set up phrase-based, syntax-based and/or neural machine translation systems for all 14 language pairs of this year’s evaluation campaign. We also performed neural rescoring of phrasebased systems for English-Turkish and English-Finnish.
Risk Factors for Obesity and Overfat among Primary School Children in Mashonaland West Province, Zimbabwe

Associated childhood obesity risk factors are not well established in developing countries such as Zimbabwe and this information is essential for tailored intervention development. This study aimed to identify prominent risk factors for overweight/obese and overfat/obese among primary school children of Mashonaland West Province in Zimbabwe. A school-based cross-sectional study was conducted using multi-stage random cluster sampling approach (30 × 30). Bivariate and multivariable logistic regression was employed and identified the risk factors for overweight/obese and overfat/obese. A total of 974 participants were enrolled in the study. Prominent significant risk factors of overweight/obese after multivariable adjustment were higher socio-economic households; parental diabetes status; and living in Makonde, Zvimba, Sanyati or Mhondoro-Ngezi district as opposed to Hurungwe district. Risk factors for overfat/obese that remained statically significant were children in urban areas (aOR = 3.19, 95% CI: 2.18−4.66, p = 0.000), being one child in a household, and parents who have diabetes mellitus. Living in Makonde, Sanyati, and Zvimba district remained associated with overfat/obese compared to Hurungwe district. This study has identified prominent proximal determinants of overweight/obese and overfat/obese among primary school children in Zimbabwe, to better assist policy guidance. Aggressive education on good nutrition activities should be tailored and targeted to most affected urban areas within high-risk districts.
Protecting Outsourced Data Privacy with Lifelong Policy Carrying

The lack of remote data access control capability and the loss of remote data access trail make data owners hesitate when they have to outsource their sensitive data to remote third party platform. The data owners have no choice but to trust the remote third party software before they ship their data to the remote environment. In this paper we propose a new set of guiding principles for protecting outsourced data with data owner specified policy. Compared with traditional access control mechanism equipped by service providers, which can be regarded as the first layer of confinement, we aim to provide data owner a second layer of confinement on data propagation and access without modifying existing data-access applications. This is achieved by two critical techniques: (1) a policy-carrying data model that binds customer data with logical data access policy, and (2) a remote application running environment which acts as data access verifier and propagation controller. To demonstrate the feasibility of this approach, we build the logical data propagation and access control (LDPAC) system, in which a human-readable policy abstract is provided to formulate data propagation and access. When policy-carrying data is shipped to remote service provider, the per-node LDPAC verifier module conducts the logical proof checking to mediate sensitive data access. Meanwhile, the authorized application which intends to access sensitive data is forced to run in an application container, in order to prevent sensitive data leakage through in-memory data breaches. Our evaluation shows that LDPAC system adds reasonable performance overhead for the remote sensitive data access and propagation mediation, while preserving the original service deployment.
SPECIATION AND ECOLOGY REVISITED: PHYLOGENETIC NICHE CONSERVATISM AND THE ORIGIN OF SPECIES

Abstract Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.
Influence of fire severity on plant regeneration by means of remote sensing imagery

In this paper we analyse the interactions between fire severity (plant damage) and plant regeneration after fire by means of remote sensing imagery and a field fire severity map. A severity map was constructed over a large fire (2692 ha) occurring in July 1994 in the Barcelona province (north-east of Spain). Seven severity classes were assigned to the apparent plant damage as a function of burning intensity. Several Landsat TM and MSS images from dates immediately before and after the fire were employed to monitor plant regeneration processes as well as to evaluate the relationship with fire severity observed in situ . Plant regeneration was monitored using NDVI measurements (average class values standardized with neighbour unburned control plots). Pre-fire NDVI measurements were extracted for every plant cover category (7), field fire severity class (7), and spatial cross-tabulation of both layers (33) and compared to post-fire values. NDVI decline due to fire was positively correlated with field fire severity class. Results show different patterns of recovery for each dominant species, severity class and combination of both factors. For all cases a significant negative correlation was found between damage and regeneration ability. This work leads to a better understanding of the influence of severity, a major fire regime parameter on plant regeneration, and may aid to manage restoration on areas burned under different fire severity levels.
Mechanism of β4 Subunit Modulation of BK Channels

Large-conductance (BK-type) Ca2+-activated potassium channels are activated by membrane depolarization and cytoplasmic Ca2+. BK channels are expressed in a broad variety of cells and have a corresponding diversity in properties. Underlying much of the functional diversity is a family of four tissue-specific accessory subunits (β1–β4). Biophysical characterization has shown that the β4 subunit confers properties of the so-called “type II” BK channel isotypes seen in brain. These properties include slow gating kinetics and resistance to iberiotoxin and charybdotoxin blockade. In addition, the β4 subunit reduces the apparent voltage sensitivity of channel activation and has complex effects on apparent Ca2+ sensitivity. Specifically, channel activity at low Ca2+ is inhibited, while at high Ca2+, activity is enhanced. The goal of this study is to understand the mechanism underlying β4 subunit action in the context of a dual allosteric model for BK channel gating. We observed that β4's most profound effect is a decrease in Po (at least 11-fold) in the absence of calcium binding and voltage sensor activation. However, β4 promotes channel opening by increasing voltage dependence of Po-V relations at negative membrane potentials. In the context of the dual allosteric model for BK channels, we find these properties are explained by distinct and opposing actions of β4 on BK channels. β4 reduces channel opening by decreasing the intrinsic gating equilibrium (L0), and decreasing the allosteric coupling between calcium binding and voltage sensor activation (E). However, β4 has a compensatory effect on channel opening following depolarization by shifting open channel voltage sensor activation (Vho) to more negative membrane potentials. The consequence is that β4 causes a net positive shift of the G-V relationship (relative to α subunit alone) at low calcium. At higher calcium, the contribution by Vho and an increase in allosteric coupling to Ca2+ binding (C) promotes a negative G-V shift of α+β4 channels as compared to α subunits alone. This manner of modulation predicts that type II BK channels are downregulated by β4 at resting voltages through effects on L0. However, β4 confers a compensatory effect on voltage sensor activation that increases channel opening during depolarization.
A Method to Prepare Solid Lipid Nanoparticles with Improved Entrapment Efficiency of Hydrophilic Drugs

Introduction: Premise of the present study was to suitably select or modify the constitution of the lipid matrix to achieve sig- nificantly high entrapment of hydrophilic drugs within solid lipid nanoparticles (SLNs). Methods and Materials: Isoniazid was selected as a representative hydrophilic drug with a high solubility of 230 mg/ml and a log P of -0.402 at 25°C (determined as per OECD TG 105 and 107 respectively). Three lipids/fatty acids (Glyceryl monostearate, Compritol 888 ATO ® and stearic acid) were evaluated out of which Compritol 888 ATO ® and stearic acid showed favorable interactions (FTIR and DSC studies) with isoniazid. The two lipids were used alone or in combination for preparing SLNs. Formulation of SLNs by microemulsification, method involved pouring the hot micro- emulsion into cold water under constant stirring, which may result in expulsion of the hydrophilic drug from the lipid matrix; hence, par- titioning of isoniazid from the hot lipid melts into cold water was also determined. Results and Discussion: Results indicate that combin- ing stearic acid with Compritol 888 ATO ® in certain ratio (1:4) led to significant entrapment efficiency (EE) of 84.0±1.1%. The formula- tions were subjected to morphological, physiochemical and in vitro drug release studies. Developed SLNs were found to be stable for 1 year at 4 °C. Conclusion: The study demonstrates the benefit of excipient screening techniques in improving entrapment efficiency of a hydrophilic drug.
Cytokinetic Abscission: Phosphoinositides and ESCRTs Direct the Final Cut

Cytokinetic abscission involves the fine and regulated recruitment of membrane remodeling proteins that participate in the abscission of the intracellular bridge that connects the two dividing cells. This essential process is mediated by the concomitant activity of the endosomal sorting complex required for transport (ESCRT) and the vesicular trafficking directed to the midbody. Phosphoinositides (PtdIns), produced at plasma membrane, and endosomes, act as molecular intermediates by recruiting effector proteins involved in multiple cellular processes, such as intracellular signaling, endo‐ and exo‐cytosis, and membrane remodeling events. Emerging evidences suggest that PtdIns have an active role in recruiting key elements that control the stability and the remodeling of the cytoskeleton from the furrow ingression to the abscission, at the end of cytokinesis. Accordingly, a possible concomitant and coordinated activity between PtdIns production and ESCRT machinery assembly could also exist and recent findings are pointing the attention on poorly understood ESCRT subunits potentially able to associate with PtdIns rich membranes. Although further studies are required to link PtdIns to ESCRT machinery during abscission, this might represent a promising field of study. J. Cell. Biochem. 118: 3561–3568, 2017. © 2017 Wiley Periodicals, Inc.
An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome

Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes. Currently, the identification of collinear segments has mainly been based on conservation of gene order and orientation. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons. Results: Using the localized LASTZ/MULTIZ analysis pipeline, we aligned 15 genomes, including cucumber and other related angiosperm plants, and identified a set of genomic segments that are short in length, stable in structure, uniform in distribution and highly conserved across all 15 plants. Compared with protein-coding genes, these conserved segments were more suitable for use as genomic markers for detecting collinear segments among distantly divergent plants. Guided by this set of identified collinear genomic segments, we inferred 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperm species, which were used as proxies for transferring functional terms to cucumber genes from the annotations of the other 14 genomes. In total, 10,885 protein-coding genes were assigned Gene Ontology (GO) terms which was nearly 1,300 more than results collected in Uniprot-proteomic database. Our results showed that annotation accuracy would been improved compared with other existing approaches. Conclusions: In this study, we provided an alternative resource for the functional annotation of predicted cucumber protein-coding genes, which we expect will be beneficial for the cucumber's biological study, accessible from http://cmb.bnu. edu.cn/functional_annotation. Meanwhile, using the cucumber reference genome as a case study, we presented an efficient strategy for transferring gene functional information from previously well-characterized protein-coding genes in model species to newly sequenced or “non-model” plant species.
Multi-band frequency compression for sensorineural hearing impairment

Sensorineural hearing loss is associated with widening of the auditory filters, leading to increased spectral masking and degraded speech perception. Multi-band frequency compression can be used for reducing the effect of spectral masking. The speech spectrum is divided into a number of bands and spectral samples in each of these bands are compressed towards the band center, by a constant compression factor. In the present study, we have investigated the effectiveness of the scheme for different compression factors, in improving the speech perception. Evaluation of the scheme using the modified rhyme test showed maximum improvement in recognition scores for compression factor of 0.6: about 17 % for the normal-hearing subjects under simulated hearing loss, and 6–21 % for the subjects with moderate to severe sensorineural hearing loss.
The effect of twice daily kiwifruit consumption on periodontal and systemic conditions before and after treatment: A randomized clinical trial

BACKGROUND To assess the nutraceutical effects of twice/daily intake of kiwifruit on periodontal parameters and systemic health before and after initial periodontal treatment (IPT). METHODS At baseline, participants were randomly assigned to test and control group, and either consumed two kiwifruits/day for 5 months or no kiwifruit. In the first 2 months, no periodontal treatment was delivered (2 M). Subsequently, a session of full-mouth IPT within 24 hours was performed. Participants were then re-assessed after 3 months (5 M). Blood samples, evaluating systemic biomarkers and vital signs, were also collected atbaseline, 2 M, and 5 M. RESULTS Groups were balanced at baseline. At 2 M no within-groups differences could be detected for any parameter but the bleeding score, which decreased significantly in the kiwifruit group by 6.67% ± 11.90% (P < 0.01). Comparison of test and control group showed that 2 months of kiwifruit consumption resulted in significant lower values of bleeding, plaque, and attachment loss. After IPT both groups demonstrated substantial significant clinical benefits however the control group showed significant greater reductions of bleeding, plaque and attachment loss than the test group. Systemic biomarkers and vital signs did not show clinically relevant differences between test and control group. CONCLUSIONS Kiwifruit consumption reduces gingival inflammation despite the lack of any periodontal instrumentation or patient's behavioral changes. No adjunctive effect to periodontal treatment of dietary intake of kiwifruit was noted. (NCT NCT03084484).
Effectively Indexing the Uncertain Space

With the rapid development of various optical, infrared, and radar sensors and GPS techniques, there are a huge amount of multidimensional uncertain data collected and accumulated everyday. Recently, considerable research efforts have been made in the field of indexing, analyzing, and mining uncertain data. As shown in a recent book on uncertain data, in order to efficiently manage and mine uncertain data, effective indexing techniques are highly desirable. Based on the observation that the existing index structures for multidimensional data are sensitive to the size or shape of uncertain regions of uncertain objects and the queries, in this paper, we introduce a novel R-Tree-based inverted index structure, named UI-Tree, to efficiently support various queries including range queries, similarity joins, and their size estimation, as well as top-k range query, over multidimensional uncertain objects against continuous or discrete cases. Comprehensive experiments are conducted on both real data and synthetic data to demonstrate the efficiency of our techniques.
The Mechanobiology of Aging Jude

Aging is a complex, multifaceted process that induces a myriad of physiological changes over an extended period of time. Aging is accompanied by major biochemical and biomechanical changes at macroscopic and microscopic length scales that affect not only tissues and organs but also cells and subcellular organelles. These changes include transcriptional and epigenetic modifications; changes in energy production within mitochondria; and alterations in the overall mechanics of cells, their nuclei, and their surrounding extracellular matrix. In addition, aging influences the ability of cells to sense changes in extracellular-matrix compliance (mechanosensation) and to transduce these changes into biochemical signals (mechanotransduction). Moreover, following a complex positive-feedback loop, aging is accompanied by changes in the composition and structure of the extracellular matrix, resulting in changes in the mechanics of connective tissues in older individuals. Consequently, these progressive dysfunctions facilitate many human pathologies and deficits that are associated with aging, including cardiovascular, musculoskeletal, and neurodegenerative disorders and diseases. Here, we critically review recent work highlighting some of the primary biophysical changes occurring in cells and tissues that accompany the aging process. 113 Click here to view this article's online features: • Download figures as PPT slides • Navigate linked references • Download citations • Explore related articles • Search keywords ANNUAL REVIEWS Further A nn u. R ev . B io m ed . E ng . 2 01 5. 17 :1 13 -1 41 . D ow nl oa de d fr om w w w . a nn ua lr ev ie w s. or g A cc es s pr ov id ed b y Jo hn s H op ki ns U ni ve rs ity o n 12 /0 7/ 15 . F or p er so na l u se o nl y. BE17CH05-Wirtz ARI 10 November 2015 14:32 ECM: extracellular matrix