Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental demonstration of passive acoustic imaging in the human skull cavity using CT-based aberration corrections.

PURPOSE Experimentally verify a previously described technique for performing passive acoustic imaging through an intact human skull using noninvasive, computed tomography (CT)-based aberration corrections Jones et al. [Phys. Med. Biol. 58, 4981-5005 (2013)]. METHODS A sparse hemispherical receiver array (30 cm diameter) consisting of 128 piezoceramic discs (2.5 mm diameter, 612 kHz center frequency) was used to passively listen through ex vivo human skullcaps (n = 4) to acoustic emissions from a narrow-band fixed source (1 mm diameter, 516 kHz center frequency) and from ultrasound-stimulated (5 cycle bursts, 1 Hz pulse repetition frequency, estimated in situ peak negative pressure 0.11-0.33 MPa, 306 kHz driving frequency) Definity™ microbubbles flowing through a thin-walled tube phantom. Initial in vivo feasibility testing of the method was performed. The performance of the method was assessed through comparisons to images generated without skull corrections, with invasive source-based corrections, and with water-path control images. RESULTS For source locations at least 25 mm from the inner skull surface, the modified reconstruction algorithm successfully restored a single focus within the skull cavity at a location within 1.25 mm from the true position of the narrow-band source. The results obtained from imaging single bubbles are in good agreement with numerical simulations of point source emitters and the authors' previous experimental measurements using source-based skull corrections O'Reilly et al. [IEEE Trans. Biomed. Eng. 61, 1285-1294 (2014)]. In a rat model, microbubble activity was mapped through an intact human skull at pressure levels below and above the threshold for focused ultrasound-induced blood-brain barrier opening. During bursts that led to coherent bubble activity, the location of maximum intensity in images generated with CT-based skull corrections was found to deviate by less than 1 mm, on average, from the position obtained using source-based corrections. CONCLUSIONS Taken together, these results demonstrate the feasibility of using the method to guide bubble-mediated ultrasound therapies in the brain. The technique may also have application in ultrasound-based cerebral angiography.
Environmental and genetic modulation of the phenotypic expression of antibiotic resistance

Abstract Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.
A new ranking method for efficient units in Data Envelopment Analysis with Expanded Feasible Region

Scholars have proposed many methods of Data Envelopment Analysis (DEA) for re-ranking already. However, in many re-ranking methods, some cannot guarantee to effectively re-rank the decision making units (DMUs) which have the same efficiency. In this research, we would propose a method that can guarantee to be completely re-ranking. Through further investigating and originally research, the Expanded Feasible Region Method for re-ranking is proposed by this research. This method not only has the function of re-ranking, it can also attest the thought that decreasing number of input items or output items can increase the discrimination of efficiency. To proof the efficiency of the method mentioned in this research, we will not only give examples to explain the method of re-ranking, but also proposes one theorem and two corollaries to prove it, showing the accuracy of the concept adduced in this research.
Identification and Isolation of Genes Involved in Poly(β-Hydroxybutyrate) Biosynthesis in Azospirillum brasilense and Characterization of a phbC Mutant

ABSTRACT Like many other prokaryotes, rhizobacteria of the genus Azospirillum produce high levels of poly(β-hydroxybutyrate) (PHB) under suboptimal growth conditions. Utilization of PHB by bacteria under stress has been proposed as a mechanism that favors their compatible establishment in competitive environments, thus showing great potential for the improvement of bacterial inoculants for plants and soils. The three genes that are considered to be essential in the PHB biosynthetic pathway, phbA (β-ketothiolase), phbB (acetoacetyl coenzyme A reductase), and phbC (PHB synthase), were identified in Azospirillum brasilense strain Sp7, cloned, and sequenced. The phbA, -B, and -C genes were found to be linked together and located on the chromosome. An A. brasilense phbC mutant was obtained by insertion of a kanamycin resistance cassette within the phbC gene. No PHB production was detected in this mutant. The capability of the wild-type strain to endure starvation conditions was higher than that of the mutant strain. However, motility, cell aggregation, root adhesion, and exopolysaccharide (EPS) and capsular polysaccharide (CPS) production were higher in the phbC mutant strain than in the wild type.
Social Divisiveness and Conflicts: Grievances Matter!

Somehow paradoxically, it is common for research on the determinants of civil wars to conclude that social factors matter much less, if at all, than economic factors. We contribute to this debate by conducting an original empirical analysis in which we investigate whether the deliberate unequal treatment of groups of people by a government can give rise to movements opposing the current political system. In doing so, we significantly innovate on the existing literature exploring the links between grievances and civil war. We look at all forms of social conflict, violent and non-violent, high and low intensity. Our index of social divisiveness captures multiple dimensions of observed unequal group treatments and is not restricted to latent ethnic divisions. We control for time-invariant factors in a large sample of countries over a long period of time. We take into account measurement uncertainty, dynamics, cross-region heterogeneity, localised spatial effects, non-linearity of effects, and a potential endogeneity bias. Our results show that social divisiveness has a large, positive, and statistically significant robust effect on anti-system opposition. It also appears to be the main channel through which long-lasting ethnic polarisation influences the onset of civil wars.
Cell-Cycle Reentry and Cell Death in Transgenic Mice Expressing Nonmutant Human Tau Isoforms

Mutations in the microtubule-associated protein tau gene have been linked to neurofibrillary tangle (NFT) formation in several neurodegenerative diseases known as tauopathies; however, no tau mutations occur in Alzheimer's disease, although this disease is also characterized by NFT formation and cell death. Importantly, the mechanism of tau-mediated neuronal death remains elusive. Aged mice expressing nonmutant human tau in the absence of mouse tau (htau mice) developed NFTs and extensive cell death. The mechanism of neuron death was investigated in htau mice, and surprisingly, the presence of tau filaments did not correlate directly with death within individual cells, suggesting that cell death can occur independently of NFT formation. Our observations show that the mechanism of neurodegeneration involved reexpression of cell-cycle proteins and DNA synthesis, indicating that nonmutant tau pathology and neurodegeneration may be linked via abnormal, incomplete cell-cycle reentry.
Clustering with Noisy Queries

In this paper, we initiate a rigorous theoretical study of clustering with noisy queries (or a faulty oracle). Given a set of $n$ elements, our goal is to recover the true clustering by asking minimum number of pairwise queries to an oracle. Oracle can answer queries of the form : "do elements $u$ and $v$ belong to the same cluster? " -- the queries can be asked interactively (adaptive queries), or non-adaptively up-front, but its answer can be erroneous with probability $p$. In this paper, we provide the first information theoretic lower bound on the number of queries for clustering with noisy oracle in both situations. We design novel algorithms that closely match this query complexity lower bound, even when the number of clusters is unknown. Moreover, we design computationally efficient algorithms both for the adaptive and non-adaptive settings. The problem captures/generalizes multiple application scenarios. It is directly motivated by the growing body of work that use crowdsourcing for {\em entity resolution}, a fundamental and challenging data mining task aimed to identify all records in a database referring to the same entity. Here crowd represents the noisy oracle, and the number of queries directly relates to the cost of crowdsourcing. Another application comes from the problem of {\em sign edge prediction} in social network, where social interactions can be both positive and negative, and one must identify the sign of all pair-wise interactions by querying a few pairs. Furthermore, clustering with noisy oracle is intimately connected to correlation clustering, leading to improvement therein. Finally, it introduces a new direction of study in the popular {\em stochastic block model} where one has an incomplete stochastic block model matrix to recover the clusters.
Fine‐mapping of two differentiated thyroid carcinoma susceptibility loci at 9q22.33 and 14q13.3 detects novel candidate functional SNPs in Europeans from metropolitan France and Melanesians from New Caledonia

Incidence of differentiated thyroid carcinoma varies considerably between countries and ethnic groups, with particularly high incidence rates in Melanesians of New Caledonia. Differentiated thyroid cancer (DTC) has a familial relative risk higher than other cancers, highlighting the contribution of inherited factors to the disease. Recently, genome‐wide association studies (GWAS) identified several DTC susceptibility loci. The most robust associations were reported at loci 9q22 (rs965513 and rs1867277) and 14q13 (rs944289 and rs116909734). In this study, we performed a fine‐mapping study of the two gene regions among Europeans and Melanesians from Metropolitan France and New Caledonia. We examined 81 single nucleotide polymorphisms (SNPs) at 9q22 and 561 SNPs at 14q13 in Europeans (625 cases/776 controls) and in Melanesians (244 cases/189 controls). The association with the four SNPs previously identified in GWAS was replicated in Europeans while only rs944289 was replicated in Melanesians. Among Europeans, we found that the two SNPs previously reported at 9q22 were not independently associated to DTC and that rs965513 was the predominant signal; at 14q13, we showed that the haplotype rs944289[C]‐rs116909374[C]‐rs999460[T] was significantly associated with DTC risk and that the association with rs116909374 differed by smoking status (p‐interaction = 0.03). Among Melanesians, a new independent signal was observed at 14q13 for rs1755774 which is strongly correlated to rs2787423; this latter is potentially a functional variant. Significant interactions with parity (p < 0.05) and body mass index were observed for rs1755774 and rs2787423. This study contributed to a better characterization of the DTC loci 9q22 and 14q13 in Europeans and in Melanesians and has identified novel variants to be prioritized for further functional studies.
The effects of climatic variation on rice production in Sri Lanka

ABSTRACT We study the responsiveness of rice production to climatic variation using a recent pseudo-panel data set from Sri Lanka. Output per farm is modelled as a non-linear function of temperature and rainfall (and other standard controls) using fixed effects regressions. We find that both climatic variables have concave, non-monotonic effects upon production, and that output is close to maximized at current climatic values. This implies that variations in growing conditions are likely to have negative effects upon production. Random simulations are used to model these impacts under various climate change scenarios, and we find that increasing temperatures will adversely affect rice production much more than varying rainfall, although the effects of a small ceteris paribus rise in temperature are positive. As rice production is a key component in economic output for Sri Lanka and other developing countries, our results have implications for food policy and poverty management in the future.
A comparison of urban school- and community-based dental clinics.

BACKGROUND The objective of the study was to quantitatively compare school- and community-based dental clinics in New York City that provide dental services to children in need. It was hypothesized that the school-based clinics would perform better in terms of several measures. METHODS We reviewed billing and visit data derived from encounter forms and expense reports from 4 school- and 3 community-based clinics during 12 months in 2004-2005. The health clinics, administered by the Children's Aid Society, provided dental services to children regardless of ability to pay. The assessments were based on 8 performance indicators, including some based on relative value units, and profile of service indicators was used for assessment. Descriptive statistics and results from hypothesis tests are reported. RESULTS Based on significant and large differences on the indicators, the school-based health clinics appear to have definite advantages over community-based dental clinics. Results were consistent across many indicators. CONCLUSIONS The results support increasing the number of school-based dental clinics in urban areas that serve children in need. Being based in schools, factors such as transportation issues, parent availability, and missed appointments are greatly reduced. This has great public dental health implications for children in underserved areas. Schools provide a natural location to provide preventive and responsive dental care. Similar advantages could be expected in rural areas and other areas of need.
Someone to talk to? The role of loneliness as a factor in the frequency of GP consultations.

BACKGROUND There are many reasons why people frequently consult their general practitioner (GP). Although loneliness is increasingly recognized as a problem affecting well-being for elderly people, it has rarely been addressed as a predictor of frequency of consultation. AIM To examine whether loneliness is associated with rates of GP consultations (home and surgery visits). METHOD Analysis of data collected in face-to-face interviews at the second wave of a longitudinal health survey of two adult age cohorts living in four socially contrasting urban localities in Glasgow City. There were a total of 691 subjects: 142 males and 176 females aged 40 years at interview; and 167 males and 206 females aged 60 years at interview. Frequency of reported GP consultations in the past 12 months at home or in the surgery was examined. RESULTS After controlling for sociodemographic and socioeconomic variables and health, loneliness was significantly associated with frequency of consultation at the surgery but not with the frequency of home visits. CONCLUSION Loneliness may still be underestimated as a factor related independently to frequency of consultations with a GP at the surgery.
Dabigatran for the treatment of venous thromboembolism

Venous thromboembolism (VTE) is a major cause of morbidity and mortality, and individuals with a first VTE are at risk of recurrent VTE. VTE treatment is divided into three phases: a first short phase of acute (traditionally parenteral) anticoagulation, followed by a second maintenance phase with an oral anticoagulant, which may be continued into a third extended maintenance phase in patients considered to be at increased risk of recurrent VTE. Vitamin K antagonists are effective oral anticoagulants but have well-known limitations; non-vitamin K oral anticoagulants including dabigatran etexilate (DE) were therefore developed. DE was approved for VTE treatment on the basis of an extensive clinical trial program that evaluated DE during both the maintenance phase and the extended maintenance phase of VTE treatment. This article provides a comprehensive overview of DE in VTE treatment, from its preclinical characteristics and pharmacokinetic properties to its efficacy and safety in major clinical trials.
Financial Innovation and Economic Growth: Empirical Evidence from China, India and Pakistan

This study investigates the causal relationship between financial innovation and economic growth in China, India, and Pakistan over the period of 1970-2016. Using an Auto-regressive Distributed Lag (ARDL) bound testing and Granger causality-based Error Correction Model (ECM), this study finds that financial innovation generally has a positive and statistically significant impact on economic growth in the short-run and long-run. This results show that in the long-run, monetary management and credit flow to the private sector play an essential role in economic growth. The trade openness and gross capital formation contribute considerably to the economic growth in China, India, and Pakistan. For robustness, this study also applies the Dynamic Ordinary Least square (DOLS) and Fully Modified Ordinary Least Square (FMOLS) method. The findings of this study suggest that financial sector plays an important role in supporting innovation activity in Asian countries.
Intraarterially delivered human umbilical cord blood‐derived mesenchymal stem cells in canine cerebral ischemia

The present study examined the effects of human umbilical cord blood‐derived mesenchymal stem cells (HUCB‐derived MSCs) delivered through the basilar artery in a canine thromboembolic brain ischemia model. Cerebral ischemia was induced through occlusion of the middle cerebral artery by injecting thrombus emboli into 10 beagles. In the HUCBC group (n = 5), 1 × 106 HUCB‐derived MSCs were transplanted through the basilar artery 1 day after ischemic induction using an endovascular interventional approach. In the control group (n = 5), phosphate‐buffered saline (PBS) was injected in the same manner in as the HUCBC group. Upon neurobehavioral examination, earlier recovery was observed in the HUCBC group. The HUCBC group showed a decrease in the infarction volume at 1 week after cerebral ischemic induction, whereas the control group showed an increase in the infarction volume at 1 week, by magnetic resonance image analysis. Transplanted cells had differentiated into neurons and astrocytes and were observed in and around endothelial cells that were positive for von Willebrand factor (vWF). HUCB‐derived MSCs expressed neuroprotective factors, such as brain‐derived neurotrophic factor (BDNF) and vascular endothelial growth factor (VEGF), at 4 weeks after the transplantation. The transplanted cells demonstrated their efficacy by reducing the infarction lesion volume and through earlier recovery from the neurological deficit. These results suggest that intraarterial transplantation of HUCB‐derived MSCs could be useful in clinical treatment of cerebral ischemia. © 2009 Wiley‐Liss, Inc.
Challenger parties in Parliament: the case of the Italian Five Star Movement

In 2013, the Five Star Movement (M5S) won representation for the first time in the Italian parliament, the heart of the institutions they criticised and aimed to reform. With parliamentary ranks filled mostly with inexperienced politicians and a strong identification with the role of outsiders challenging the mainstream political consensus, the expectation is that their opposition style should differ substantially from that of other parties. This article explores this question by comparing the policy content of oral parliamentary questions submitted by the M5S with that of other Italian opposition parties during the 17th legislature (2013-2018). It analyses to what extent the M5S’s issue profile 1) overlaps more with parties of either the left or the right side of the political spectrum, 2) is more likely to deal with matters emphasised in its electoral platform, and 3) is more likely to address issues not attended to by other parties. The results provide new insights into the behaviour of new challenger parties in parliament.
Measuring protein‐protein interactions inside living cells using single color fluorescence correlation spectroscopy. Application to human immunodeficiency virus type 1 integrase and LEDGF/p75

Recently we described the interaction of human immunodeficiency virus type 1 (HIV‐1)1 integrase (IN) with a cellular protein, lens epithelium‐derived growth factor/transcription co‐activator p75 (LEDGF/p75). We now present the study of the diffusion behavior of the three independent domains of IN and LEDGF/p75 using fluorescence correlation microscopy (FCM). We show that diffusion in the cell of the different enhanced green fluorescent protein (EGFP) fusion proteins is described by two components with different fractions and that the average parameters in the nucleus are comparable with those in the cytoplasm. In addition, we demonstrate that specific interaction between EGFP‐fused HIV‐1 IN and LEDGF/p75 results in a shift in diffusion coefficient (D). The opposite shift was observed in an IN‐deletion mutant that does not exhibit LEDGF/p75 binding or in a LEDGF/p75 knock‐down experiment using siRNA. We thus demonstrate that protein–protein interactions can be studied in living cells, using single‐color FCM (scFCM).
Studies on human migration inhibitory factor: characterization of three molecular species.

Human migration inhibitory factor (MIF), obtained from supernatants of peripheral blood mononuclear cells stimulated with concanavalin A, was analyzed by gel filtration, isoelectrofocusing, and CsCl density gradient centrifugation. A distinct pattern of heterogeneity was determined on the basis of its harvesting time and biochemical criteria. Supernatants from cells cultured for 1 day contained a single peak of MIF activity with an isoelectric point of 4.3 to 5.2, an apparent m.w. of 23,000, and a density of 1.314 g/ml, the same as the density of the marker protein, 125I-HSA (1st day pH 5-MIF). Furthermore, this species of human MIF was sensitive to treatment with trypsin, strongly suggesting its being a protein, but not to treatment with neuraminidase and corresponds therefore to guinea pig pH 5-MIF. However, when 2nd day supernatants were analyzed under the same conditions, 2 MIF species were found. One species with an isoelectric point of 2.4 to 3.3 had an apparent m.w. of 65,000 (2nd day 3-MIF). The other species with an isoelectric point of 4.3 to 5.6 had an apparent m.w. of 23-43,000 (2nd day pH 5-MIF). Upon centrifugation in CsCl density gradients, the density (rho 25 of 1.314 to 1.414 g/ml) of both species was found to be greater than that of the pure protein, 125I-HSA. In addition, both species were chymotrypsin and neuraminidase sensitive but not trypsin sensitive, further suggesting their glycoprotein nature.