Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Supernumerary B Chromosomes in Drosophila melanogaster

B chromosomes are small, heterochromatic chromosomes that are transmitted in a non-Mendelian manner. We have identified a stock of Drosophila melanogaster that recently (within the last decade) acquired an average of 10 B chromosomes per fly. These B chromosomes are transmitted by both males and females and can be maintained for multiple generations in a wild-type genetic background despite the fact that they cause high levels of 4th chromosome meiotic nondisjunction in females. Most curiously, these B chromosomes are mitotically unstable, suggesting either the absence of critical chromosomal sites or the inability of the meiotic or mitotic systems to cope with many additional chromosomes. These B chromosomes also contain centromeres and are primarily composed of the heterochromatic AATAT satellite sequence. Although the AATAT sequence comprises the majority of the 4th chromosome heterochromatin, the B chromosomes lack most, if not all, 4th chromosome euchromatin. Presumably as a consequence of their heterochromatic content, these B chromosomes significantly modify position-effect variegation in two separate reporter systems, acting as enhancers of variegation in one case and suppressors in the other. The identification of B chromosomes in a genetically tractable organism like D. melanogaster will facilitate studies of chromosome evolution and the analysis of the mechanisms by which meiotic and mitotic processes cope with additional chromosomes.
Computing Semantic Change Using Context Volatility

In this paper we describe problems occurring while modeling the dynamics of terminology context in diachronic corpora and how to solve them. The foundation for this work is context volatility, a measurement for contextual change [4], that we use as our main measuring unit. The computation of context volatility for a word relies on the significance-values of its co-occurrent terms and the corresponding co-occurrence ranks. In the ongoing process its necessary to evaluate these ranks precisely. After applying context volatility according to [4] it can be shown that there are many cases for which a co-occurrence of two words at a specific point of time has no joint occurrence of its terms in other time stamps. This leaves gaps in the assigned ranks for the co-occurrences which must be handled accordingly. Just setting an arbitrary rank is not accompanied by a reasonable model. In this paper we present solutions and ideas to overcome this problem. We show that the use of very sparse term-term matrices leads to undesired results. We use corpus level statistics and a recommender system to recalculate frequencies and co-occurrence statistics on the time slices. Within such a setting we can use the measure context volatility in a way more consistent manner and we propose the idea for a well-defined statistical model based on the presented results.
Precise concrete type inference for object-oriented languages

Concrete type information is invaluable for program optimization. The determination of concrete types in object-oriented languages is a flow sensitive global data flow problem. It is made difficult by dynamic dispatch (virtual function invocation) and first class functions (and selectors)—the very program structures for whose optimization its results are most critical. Previous work has shown that constraint-based type inference systems can be used to safely approximate concrete types [15], but their use can be expensive and their results imprecise. We present an incremental constraint-based type inference which produces precise concrete type information for a much larger class of programs at lower cost. Our algorithm extends the analysis in response to discovered imprecisions, guiding the analysis' effort to where it is most productive. This produces precise information at a cost proportional to the type complexity of the program. Many programs untypable by previous approaches or practically untypable due to computational expense, can be precisely analyzed by our new algorithm. Performance results, precision, and running time, are reported for a number of concurrent object-oriented programs. These results confirm the algorithm's precision and efficiency.
A semantic information retrieval model for focused crawling

Nowadays, users of computers store a lot of information on the Web. For this reason, the Internet is a good place to search information on any subject. Due to the large amount of information, some users would search information on specific websites that they consider interesting (e.g. www.wikipedia.com, news sites, etc.). Traditional models represent webpages by using the frequency of terms or the structure of links in order to assign weight to terms of webpages. This paper presents a semantic information retrieval to represent specific websites. This proposal integrates text mining algorithms based on natural language processing and traditional representation models with the aim to improve the quality of webpages recovered by searching. Each webpage of the website is represented as a vector of topics, instead of a vector of terms. In a similar way, the query is represented as a vector of topics. Thus, a similarity measure can be applied over this vector and vectors of documents to retrieve the most relevant documents.
Social work - client relationship practice: exploring social worker perspectives

This thesis explores, using qualitative methodology, the significance of social worker – client relationships for achieving client outcomes in the field of child and family welfare. The study found that social worker – client relationships are critical for achieving outcomes. It is a distinct practice method, informed by relational views about ‘the self’, human development and healing. The social worker, as Relationship Building Agent, is heavily focused on client engagement and building the Relationship Workspace. These findings are represented in the approach Social Work Relationship Praxis. Implications for social work practice, education and research include recommended elevation of relational perspectives.
Towards Trust Engineering for Opportunistic Cloud Services: A Systematic Review of Trust Engineering in Cloud Computing

The systematic review methodology has been employed to review trust related studies in cloud computing. It was observed that trusted computing technologies and reputation based approaches are the main approaches to trust engineering in cloud computing. Also, trusted third party approaches and the deployment model play a significant role in enhancing trust between service providers and consumers. It was observed that the concept of trust is used loosely without any formal specification in cloud computing discussions and trust engineering in general. As a first step towards addressing this problem, we have contextualized the formal trust specification in multi-agent environments for cloud computing. Keywordssecurity engineering; trust engineering; trust in cloud computing; trust modeling.
PKU-ICST at TRECVID 2016: Instance Search Task

We participated in all two types of Instance Search (INS) task in TRECVID 2016: automatic search and interactive search. This paper presents our approaches and results. In this task, we first conducted two search processes: location-specific search and person-specific search, and then the score fusion of the two processes was performed to get the final results. In the location-specific search process, we adopted two kinds of features: (1) Bag-of-Words (BoW) feature based on Approximate K-means (AKM); and (2) DNN feature based on Convolutional Neural Networks (CNN). In the person-specific search process, we adopted three kinds of methods, including (1) face recognition; (2) person re-identification; and (3) text-based search. After getting the results of location-specific and person-specific search, we conducted instance score fusion with two strategies: searching a given person based on location-specific results, and searching a given location based on person-specific results. In the re-ranking stage, we further applied semi-supervised learning based re-ranking method to improve the search results. The official evaluations showed that our team ranked 1 st in both automatic search and interactive search.
Novel overload controls for SIP networks

The increasing use of SIP in Next Generation Networks necessitates that SIP networks provide adequate control mechanisms to optimize transaction throughput and prevent congestion collapse during traffic overloads. SIP elements need well behaved internal overload controls to detect and throttle traffic, and external controls between SIP elements are needed to throttle traffic closer to the source. This paper presents the results of simulations that demonstrate the inadequacy of current SIP controls, and then presents several novel algorithms to control SIP network overloads. We show our new algorithms increase goodput across increasing load levels, are robust to IP loss and delay, and perform well under transient burst loads.
Expression of CD30 in patients with acute graft-versus-host disease.

Acute GVHD (aGVHD) remains a major source of morbidity after allogeneic hematopoietic cell transplantation. CD30 is a cell-surface protein expressed on certain activated T cells. We analyzed CD30 expression on peripheral blood T-cell subsets and soluble CD30 levels in 26 patients at the time of presentation of aGVHD, before the initiation of treatment, compared with 27 patients after hematopoietic cell transplantation without aGVHD (NONE). Analysis by flow cytometry showed that patients with aGVHD had a greater percentage of CD30 expressing CD8(+) T cells with the difference especially pronounced in the central memory subset (CD8(+)CD45RO(+)CD62L(+)): GVHD median 12.4% (range, 0.8%-33.4%) versus NONE 2.1% (0.7%, 17.5%), P < . 001. There were similar levels of CD30 expression in naive T cells, CD4(+) T cells, and regulatory (CD4(+)CD127(low)CD25(+)) T cells. Plasma levels of soluble CD30 were significantly greater in patients with GVHD: median 61.7 ng/mL (range, 9.8-357.1 ng/mL) versus 17.4 (range, 3.7-142.4 ng/mL) in NONE (P < .001). Immunohistochemical analysis of affected intestinal tissue showed many CD30(+) infiltrating lymphocytes present. These results suggest that CD30 expression on CD8(+) T-cell subsets or plasma levels of soluble CD30 may be a potential biomarker for aGVHD. CD30 may also represent a target for novel therapeutic approaches for aGVHD.
Current and emerging treatment options for uveal melanoma

Uveal melanoma (UM) is the most common primary malignant intraocular tumor in adults, with a 10-year cumulative metastatic rate of 34%. The most common site of metastasis is the liver (95%). Unfortunately, the current treatment of metastatic UM is limited by the lack of effective systemic therapy. Options for the management of the primary intraocular tumor include radical surgery as well as conservative treatments in order to preserve visual acuity. For metastatic disease, several approaches have been described with no standard method. Nevertheless, median survival after liver metastasis is poor, being around 4–6 months, with a 1-year survival of 10%–15%. In this review, the authors summarize current and promising new treatments for UM.
A regional general equilibrium analysis of the welfare impact of cash transfers

Using a regionally disaggregated computable general equilibrium model, we analyze the differential welfare impacts of a cash transfer program targeted at rural areas. The direct effect of the transfers decreases regional income differentials, but the indirect effects depend on how the program is financed. Financing the program with a more efficient tax system is also less regressive and has favorable urban impacts. The less efficient instruments result in relatively higher incomes in all rural regions, but are more regressive. The increasing share of urban poverty highlights the shortcomings of rural targeting and raises the issue of horizontal equity.
Coordinate-dependent diffusion in protein folding

Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the folding dynamics of small single-domain proteins. Complicating the interpretation of both simulations and experiments is the expectation that the effective diffusion coefficient D will in general depend on the position along the folding coordinate, and this dependence may vary for different coordinates. Here we explore the position dependence of D, its connection to protein internal friction, and the consequences for the interpretation of single-molecule experiments. We find a large decrease in D from unfolded to folded, for reaction coordinates that directly measure fluctuations in Cartesian configuration space, including those probed in single-molecule experiments. In contrast, D is almost independent of Q, the fraction of native amino acid contacts: Near the folded state, small fluctuations in position cause large fluctuations in Q, and vice versa for the unfolded state. In general, position-dependent free energies and diffusion coefficients for any two good reaction coordinates that separate reactant, product, and transition states, are related by a simple transformation, as we demonstrate. With this transformation, we obtain reaction coordinates with position-invariant D. The corresponding free-energy surfaces allow us to justify the assumptions used in estimating the speed limit for protein folding from experimental measurements of the reconfiguration time in the unfolded state, and also reveal intermediates hidden in the original free-energy projection. Lastly, we comment on the design of future single-molecule experiments that probe the position dependence of D directly.
Physiologic Changes during Chronic Congestive Heart Failure in Dogs with Tricuspid Insufficiency and Pulmonic Stenosis

chronic congestive heart failure was studied in dogs with surgically-produced tricuspid insufficiency and pulmonic stenosis. Ascites formed in association with an elevation in mean right atrial pressure. The volume of ascitic fluid and the rate of urinary sodium excretion varied greatly in individual dogs during the course of congestive failure and among the different animals. Sodium retention was most common but periods of sodium balance and natriuresis occurred. Comparative data on the right and left ventricles were obtained from determinations of intracardiac pressures, measurements of ventricular muscle mass at the time of sacrifice and studies of the lungs for evidence of chronic passive congestion. There was significant right ventricular hypertrophy but no evidence of left ventricular hypertrophy or failure.
Understanding teacher shortages: An analysis of teacher supply and demand in the United States

This paper reviews the sources of and potential solutions to teacher shortages in the United States. It describes the sources of current and projected increases in teacher demand relative to enrollments, shifts in pupil-teacher ratios, and attrition. It places these in relation to recent declines in teacher supply and evaluates evidence of shortages in fields like mathematics, science, special education, and educators for English learners, as well as in particular parts of the country. Our analysis using national databases through 2016 predicted an estimated annual teacher shortage of approximately 112,000 teachers in 2017-18. Our recent review of state teacher workforce reports estimated 109,000 individuals were uncertified for their teaching positions in the US in 2017, roughly approximating our projections. We discuss the factors driving shortages and, based on previous research, identify responses that might ameliorate these trends.
What-If Reasoning with Counterfactual Gaussian Processes

Answering "What if? " questions is important in many domains. For example, would a patient's disease progression slow down if I were to give them a dose of drug A? Ideally, we answer our question using an experiment, but this is not always possible (e.g., it may be unethical). As an alternative, we can use non-experimental data to learn models that make counterfactual predictions of what we would observe had we run an experiment. In this paper, we propose the counterfactual GP, a counterfactual model of continuous-time trajectories (time series) under sequences of actions taken in continuous-time. We develop our model within the potential outcomes framework of Neyman and Rubin. The counterfactual GP is trained using a joint maximum likelihood objective that adjusts for dependencies between observed actions and outcomes in the training data. We report two sets of experimental results using the counterfactual GP. The first shows that it can be used to learn the natural progression (i.e. untreated progression) of biomarker trajectories from observational data. In the second, we show how the CGP can be used for medical decision support by learning counterfactual models of renal health under different types of dialysis.
Absorption Profile of (Poly)Phenolic Compounds after Consumption of Three Food Supplements Containing 36 Different Fruits, Vegetables, and Berries

The market of plant-based nutraceuticals and food supplements is continuously growing due to the increased consumer demand. The introduction of new products with relevant nutritional characteristics represents a new way of providing bioactive compounds and (poly)phenols to consumers, becoming a strategy to ideally guarantee the health benefits attributed to plant foodstuffs and allowing the increase of daily bioactive compound intake. A paramount step in the study of nutraceuticals is the evaluation of the bioavailability and metabolism of their putatively active components. Therefore, the aim of the present study was to investigate the absorption profile of the (poly)phenolic compounds contained in three different plant-based food supplements, made of 36 different plant matrices, which were consumed by 20 subjects in an open one-arm study design. Blood samples were collected at baseline and 1, 2, 5, and 10 h after capsule intake. Twenty quantifiable metabolites deriving from different (poly)phenolic compounds were identified. Results showed that the consumption of the three capsules allowed the effective absorption of several (poly)phenolic compounds and metabolites appearing at different times in plasma, thereby indicating different absorption profiles. The capsules thus ensured potential health-promoting molecules to be potentially available to target tissues and organs.
Harmonic phase estimation in single-channel speech enhancement using von mises distribution and prior SNR

In single-channel speech enhancement the spectral amplitude of the noisy signal is often modified while the noisy spectral phase is directly employed for signal reconstruction. Recently, additional improvement in speech enhancement performance has been reported when the noisy phase is modified. In this work, we propose a Bayesian estimator for phase of harmonics given the noisy speech. The proposed estimator relies on the fundamental frequency and the signal-to-noise ratio at harmonics. Throughout our experiments, we evaluate the performance of the proposed phase enhancement in comparison with the noisy phase, a benchmark and the clean phase as the upper-bound. The proposed method leads to joint improvement in quality and intelligibility at different SNRs and noise types.
The Dam1 ring binds to the E-hook of tubulin and diffuses along the microtubule

Several models of Dam1 complex function at the kinetochore have been proposed. Here we show that removal of the E-hooks of tubulin reduces Dam1 binding 40-fold. We also report the first structure of the Dam1 ring around microtubules and evidence that this ring freely diffuses on microtubules based on imaging individual rings.
High Performance SQL Queries on Compressed Relational Database

Loss-less data compression is potentially attractive in database application for storage cost reduction and performance improvement. The existing compression architectures work well for small to large database and provide good performance. But these systems can execute a limited number of queries executed on single table. We have developed a disk-based compression architecture, called DHIBASE, to support large database and at the same time, perform high performance SQL queries on single or multiple tables in compressed form. We have compared our system with widely used Microsoft SQL Server. Our system performs significantly better than SQL Server in terms of storage requirement and query response time. DHIBASE requires 10 to 15 times less space and for some operation it is 18 to 22 times faster. As the system is column oriented, schema evolution is easy.
Brief Definitive Report

T lymphocytes are fundamental for the control of infection. In rare cases, T cell deficiencies are congenital, caused by mutations preventing the expression of any gene required for T cell generation. However, in most cases they are induced in the adult either by infections such as AIDS, by aggressive anticancer therapies, or by aging. In the current clinical practice, these situations have become frequent, rendering the reconstitution of the peripheral T cell pool an important clinical goal. In children who do not yet have competent thymus epithelia, T cell reconstitution may be achieved by the trans-plantation of a competent BM. However, because BM precursors must transit through the thy-mus to generate T cells, the peripheral T cell reconstitution is delayed by many months, during which time patients are very susceptible to infec-cannot correct T cell deficiencies once the thy-mus atrophies in adults. Thymus transplants could constitute an advantageous alternative or complementary therapy; these grafts could be a source of both a functional thymus epithelia and functional T cells, and thus might correct T cell deficiencies in both children and adults. They would not necessarily require the conditioning of the patient and should export mature T cells immediately , overcoming the long lag-time required for thymus T cell generation after BM transplantation. However, although thymus grafts were successful in correcting deficiencies of the thymus epithelium, as found in the complete DiGeorge syndrome (Markert et al., 2007) or CORRESPONDENCE Benedita Rocha:
Differences in leaves of olive trees under organic , integrated and conventional pest management

Differences in pest management of olive orchards may affect the development of olive trees and may be reflected in terms of absolute and relative asymmetry, mass, and quality of the leaves. Leaf mass and residual leaf mass of olive trees were significantly greater under organic management than other pest management regimes. The analysis revealed that leaves from trees under different pest management regimes differed, a result that may have practical applications. © 2003 Elsevier Science B.V. All rights reserved.