Miracle-dz/UniFAR-FTUs huggingface dataset:
Vibrio cholerae VpsT Regulates Matrix Production and Motility by Directly Sensing Cyclic di-GMP

Decoding a Second-Messenger's Message Biofilms are aggregates of bacteria on a surface often associated with increased resistance to antibiotics and stress. In Vibrio cholerae, the bacterial species that causes cholera, biofilm formation is promoted by the bacterial second-messenger cyclic diguanylate (c-di-GMP) and involves the transcription regulator, VpsT. Krasteva et al. (p. 866) show that VpsT is itself a receptor for c-di-GMP and that binding of the small signaling molecule promotes VpsT dimerization, which is required for DNA recognition and transcriptional regulation. As well as activating components of the biofilm pathway, VpsT also down-regulates motility genes in a c-di-GMP–dependent manner. A bacterial signaling molecule induces the dimerization and activation of a biofilm-promoting transcription factor. Microorganisms can switch from a planktonic, free-swimming life-style to a sessile, colonial state, called a biofilm, which confers resistance to environmental stress. Conversion between the motile and biofilm life-styles has been attributed to increased levels of the prokaryotic second messenger cyclic di-guanosine monophosphate (c-di-GMP), yet the signaling mechanisms mediating such a global switch are poorly understood. Here we show that the transcriptional regulator VpsT from Vibrio cholerae directly senses c-di-GMP to inversely control extracellular matrix production and motility, which identifies VpsT as a master regulator for biofilm formation. Rather than being regulated by phosphorylation, VpsT undergoes a change in oligomerization on c-di-GMP binding.
Do older adults with Alzheimer's disease engage in estate planning and advance care planning preparation?

ABSTRACT Objectives: This study investigated the estate planning and advance care planning (ACP) of older adults diagnosed with Alzheimer's disease (AD) for the presence of (1) a valid will, (2) a durable power of attorney for health care, and (3) a living will. Method: We analyzed 10,273 adults aged 65 and older from the 2012 Health and Retirement Study (HRS) using multilevel logistic regression. Results: We found that a diagnosis of AD was significantly associated with the ACP variables. Older adults with AD were more likely to assign a durable power of attorney for health care and have a written living will than older adults without an AD diagnosis. However, we found no significant association between a diagnosis of AD and having a valid will. These findings were robust when adjusting for demographic and socioeconomic variables. Other factors decreased engagement in estate planning and ACP, including lower socioeconomic status, being male, and being a minority. Conclusion: Our findings suggest that a diagnosis of AD is associated with more engagement in ACP for individuals and their families, but important barriers exist for people with fewer resources.
Kinetochore chemistry is sensitive to tension and may link mitotic forces to a cell cycle checkpoint

Some cells have a quality control checkpoint that can detect a single misattached chromosome and delay the onset of anaphase, thus allowing time for error correction. The mechanical error in attachment must somehow be linked to the chemical regulation of cell cycle progression. The 3F3 antibody detects phosphorylated kinetochore proteins that might serve as the required link (Gorbsky, G. J., and W. A. Ricketts. 1993. J. Cell Biol. 122:1311-1321). We show by direct micromanipulation experiments that tension alters the phosphorylation of kinetochore proteins. Tension, whether from a micromanipulation needle or from normal mitotic forces, causes dephosphorylation of the kinetochore proteins recognized by 3F3. If tension is absent, either naturally or as a result of chromosome detachment by micromanipulation, the proteins are phosphorylated. Equally direct experiments identify tension as the checkpoint signal: tension from a microneedle on a misattached chromosome leads to anaphase (Li, X., and R. B. Nicklas. 1995. Nature (Lond.). 373:630-632), and we show here that the absence of tension caused by detaching chromosomes from the spindle delays anaphase indefinitely. Thus, the absence of tension is linked to both kinetochore phosphorylation and delayed anaphase onset. We propose that the kinetochore protein dephosphorylation caused by tension is the all clear signal to the checkpoint. The evidence is circumstantial but rich. In any event, tension alters kinetochore chemistry. Very likely, tension affects chemistry directly, by altering the conformation of a tension-sensitive protein, which leads directly to dephosphorylation.
Do Programs for Runaway and Homeless Youth Work? A Qualitative Exploration From the Perspectives of Youth Clients in Diverse Settings

Runaway and homeless youth (RHY) comprise a large population of young people who reside outside the control and protection of parents and guardians and who experience numerous traumas and risk factors, but few buffering resources. Specialized settings have developed to serve RHY, but little is known about their effects. The present cross-sectional qualitative descriptive study, grounded in the positive youth development approach and the Youth Program Quality Assessment model, addressed this gap in the literature. From a larger sample of 29 RHY-specific settings across New York State, RHY ages 16–21 from 11 settings were purposively sampled for semi-structured in-depth interviews on their transitions into homelessness, experiences with settings, and unmet needs (N = 37 RHY). Data were analyzed with a theory-driven and inductive systematic content analysis approach. Half of participants (54%) were female; almost half (49%) identified as non-heterosexual; and 42% were African American/Black, 31% were Latino/Hispanic, and 28% were White/other. Results indicated that because RHY are a uniquely challenged population, distrustful of service settings and professional adults and skilled at surviving independently, the population-tailored approaches found in RHY-specific settings are vital to settings’ abilities to effectively engage and serve RHY. We found the following four major themes regarding the positive effects of settings: (1) engaging with an RHY setting was emotionally challenging and frightening, and thus the experiences of safety and services tailored to RHY needs were critical; (2) instrumental support from staff was vital and most effective when received in a context of emotional support; (3) RHY were skilled at survival on the streets, but benefited from socialization into more traditional systems to foster future independent living; and (4) follow-through and aftercare were needed as RHY transitioned out of services. With respect to gaps in settings, RHY highlighted the following: (1) a desire for better management of tension between youths’ needs for structure and wishes for autonomy and (2) lack of RHY input into program governance. This study advances our understanding of RHY, their service needs, and the ways settings meet these needs, as well as remaining gaps. It underscores the vital, life-changing, and even life-saving role these settings play for RHY.
Framework for Abstractive Summarization using Text-to-Text Generation

We propose a new, ambitious framework for abstractive summarization, which aims at selecting the content of a summary not from sentences, but from an abstract representation of the source documents. This abstract representation relies on the concept of Information Items (InIt), which we define as the smallest element of coherent information in a text or a sentence. Our framework differs from previous abstractive summarization models in requiring a semantic analysis of the text. We present a first attempt made at developing a system from this framework, along with evaluation results for it from TAC 2010. We also present related work, both from within and outside of the automatic summarization domain.
Exploiting workload similarities for efficient scheduling in diverse asymmetric chip multiprocessing Research

Heterogeneous chip-multiprocessor (HCMP) incorporates different types of cores on a single die. Each core-type operates in a different way, provides different capabilities, and shows different performance attributes. Asymmetric chip-multiprocessor (ACMP) is an HCMP in which all coretypes comply to the same instruction set architecture (ISA). In some ACMP design schemes cores share functional components, sometimes even mutually exclude each other. ACMPs can increase power-efficiency by executing diverse workloads on suitable cores. Matching workloads to cores with ever-changing workload behaviors is a challenge. Practical solutions so far assume ordering of core strength from simple “small” energy-efficient cores to complex “big” ones which provide high performance for compute-heavy workloads. This approach allows relatively straightforward workload-to-core assignment. While ARM-based big.LITTLE architectures already capture a huge market share, higher single-ISA diversity is avoided. In this thesis, we argue that restricting the cores design space to linear ordering limits the potential of ACMP. We examine the notion of using asymmetric specialized chip-multiprocessors (ASCMPs) to achieve better power-efficiency. Managing the execution of a multi-core system with high core and workloads diversity is a complex task. In order to perform this task efficiently, there is a need to predict the powerperformance attributes of a workload on the different cores. For this purpose, we propose a centralized history-based lookup mechanism that shares execution information among cores. During workload execution, each core produces micro-architectureindependent signatures and corresponding performance attributes. The signatures are generated using workload behavior, and not from the impact on the core. This approach guarantees that the workload signature is identical regardless of the core it runs on. The signature is created for performance characterization per core, where workloads that share the same signature are expected to have similar performance characteristics when executed on the same core. Thus, the execution management system exploits workload similarities to group workloads by behaviors and use execution information as a performance predictor. The micro-architecture-independent signature structure should be small enough (bitwise) to enable practical mechanism, use execution characteristics which are feasible to extract in addition to fulfilling two opposing requirements:
STUDY OF INFLUENCE OF FREEZING-DEFROSTING ON THERMOPHYSICAL PROPERTIES OF MEAT SYSTEMS

There were studied thermophysical properties of meat systems, based on comminuted beef with different chemical compositions in the process of freezing-defrosting. It was demonstrated, that the morphological base of meat (the ratio of muscular, connective and fatty tissues) and its chemical composition essentially influence thermophysical properties in the process of freezing-defrosting. It was revealed, that under conditions of realization of freezing-defrosting cycle with the fat mass share increase, the temperature increase of the maximal speed of crystal creation, decrease of the cryoscopic temperature interval, increase of the share of moisture that changes its aggregate state in the cryoscopic temperature interval, increase of specific heat of the phase transfer in the cryoscopic temperature interval are observed in a meat system. The type of changes of the cryoscopic temperature interval allows to detect that fat essentially influences the process of freezing-defrosting. The realized studies of comparison of thermodynamic changes in meat systems at refrigerator processing allowed to determine the strategy of saving meat systems’ stability that is in providing meat proteins’ colloid stability and renewing initial properties of the meat raw material after storage and defrosting.
6LB: Scalable and Application-Aware Load Balancing with Segment Routing

Network load-balancers generally either do not take the application state into account, or do so at the cost of a centralized monitoring system. This paper introduces a load-balancer running exclusively within the IP forwarding plane, ı.e., in an application protocol agnostic fashion – yet which still provides application-awareness and makes real-time, decentralized decisions. To that end, IPv6 Segment Routing is used to direct data packets from a new flow through a chain of candidate servers, until one decides to accept the connection, based solely on its local state. This way, applications themselves naturally decide on how to fairly share incoming connections, while incurring minimal network overhead, and no out-of-band signaling. A consistent hashing algorithm, as well as an in-band stickiness protocol, allow for the proposed solution to be able to be reliably distributed across a large number of instances. Performance evaluation by means of an analytical model and actual tests on different workloads (including a Wikipedia replay as a realistic workload) show significant performance benefits in terms of shorter response times, when compared with the traditional random load-balancer. In addition, this paper introduces and compares kernel bypass high-performance implementations of both 6LB and the state-of-the-art load-balancer, showing that the significant system-level benefits of 6LB are achievable with a negligible data-path CPU overhead.
The Millennium Villages Project : A protocol for the final evaluation

The Millennium Villages Project is a ten-year integrated rural development project implemented in ten sub-Saharan African sites. This protocol documents the final evaluation of the project, including its basic principles, site selection, and a five-part evaluation plan. The evaluation will include an adequacy assessment, impact evaluation, cost assessment, process evaluation, and description of systems design and tools. We describe data collection and analysis for each component, as well as our plan for transparency and study limitations. Taken together, this evaluation is designed to assess the Millennium Village Project’s model for achieving the Millennium Development Goals in rural sub-Saharan Africa.
HIV-1 Subtype C-Infected Individuals Maintaining High Viral Load as Potential Targets for the “Test-and-Treat” Approach to Reduce HIV Transmission

The first aim of the study is to assess the distribution of HIV-1 RNA levels in subtype C infection. Among 4,348 drug-naïve HIV-positive individuals participating in clinical studies in Botswana, the median baseline plasma HIV-1 RNA levels differed between the general population cohorts (4.1–4.2 log10) and cART-initiating cohorts (5.1–5.3 log10) by about one log10. The proportion of individuals with high (≥50,000 (4.7 log10) copies/ml) HIV-1 RNA levels ranged from 24%–28% in the general HIV-positive population cohorts to 65%–83% in cART-initiating cohorts. The second aim is to estimate the proportion of individuals who maintain high HIV-1 RNA levels for an extended time and the duration of this period. For this analysis, we estimate the proportion of individuals who could be identified by repeated 6- vs. 12-month-interval HIV testing, as well as the potential reduction of HIV transmission time that can be achieved by testing and ARV treating. Longitudinal analysis of 42 seroconverters revealed that 33% (95% CI: 20%–50%) of individuals maintain high HIV-1 RNA levels for at least 180 days post seroconversion (p/s) and the median duration of high viral load period was 350 (269; 428) days p/s. We found that it would be possible to identify all HIV-infected individuals with viral load ≥50,000 (4.7 log10) copies/ml using repeated six-month-interval HIV testing. Assuming individuals with high viral load initiate cART after being identified, the period of high transmissibility due to high viral load can potentially be reduced by 77% (95% CI: 71%–82%). Therefore, if HIV-infected individuals maintaining high levels of plasma HIV-1 RNA for extended period of time contribute disproportionally to HIV transmission, a modified “test-and-treat” strategy targeting such individuals by repeated HIV testing (followed by initiation of cART) might be a useful public health strategy for mitigating the HIV epidemic in some communities.
Assessment of bradykinesia in Parkinson's disease patients through a multi-parametric system

The aim of this paper is to describe and present the results of the automatic detection and assessment of bradykinesia in motor disease patients using wireless, wearable accelerometers. The current work is related to a module of the PERFORM system, a FP7 project from the European Commission, that aims at providing an innovative and reliable tool, able to evaluate, monitor and manage patients suffering from Parkinson's disease. The assessment procedure was carried out through a developed C# library that detects the activities of the patient using an activity recognition algorithm and classifies the data using a Support Vector Machine trained with data coming from previous test phases. The accuracy between the output of the automatic detection and the evaluation of the clinician both expressed with the Unified Parkinson's disease Rating Scale, presents an average value of [68.3±8.9]%. A meta-analysis algorithm is used in order to improve the accuracy to an average value of [74.4±14.9]%. Future work will include a personalized training of the classifiers in order to achieve a higher level of accuracy.
Sediment-Associated Elements in a Constructed Wetland Treatment System: Distribution, Characterization, and Toxicity

In a pilot-scale constructed wetland treatment system, Hg, Se, and As were removed from flue gas desulfurization wastewater through a combination of physical, chemical, and biological processes that resulted in their accumulation in the sediment. The first objective of this research was to characterize sediment-associated Hg, Se, and As into operationally-defined fractions using sequential extraction procedures. All measurements were taken after 17 months of wastewater treatment. Mercury concentrations in the sediment varied from 0.025 to 0.035 mg kg in the treatment system, while concentrations of Se and As in the sediment increased from 3.57 to 8.79 mg kg and 11.91 to 14.08 mg kg, respectively. Results suggest that Hg and As are stable, immobile, and non-bioavailable in the sediment, as long as current sediment conditions such as pH and redox potential remain stable. Approximately half of the total selenium in the sediment is mobile and bioavailable, while the other half is stable and not bioavailable to plants and organisms. Identification of the main phase associations of Hg, Se, and As in sediments helps to understand the biogeochemical processes involved and to evaluate the risk and remobilization potential of these elements in the constructed wetland. A toxicity assessment of this sediment was then performed to obtain the information needed to support environmental management decisions related to mitigating risks associated with FGD wastewater. The second objective of this research was to evaluate the toxicity of these sediments to Hyalella azteca. Despite the use of this constructed wetland treatment system to treat simulated FGD wastewater for over a year, the sediment was not toxic to H. azteca. It was apparent from this research that measuring sediment toxicity and total concentrations of Hg, Se, and As in sediment cannot provide the required information about mobility, bioavailability, and the potential impact on the aquatic system. _____________________________________________________________________________________________________________
Investigation of transient surface electric field induced by femtosecond laser irradiation of aluminum

Transient surface electric fields induced by femtosecond laser irradiation of an aluminum film were investigated directly by ultrashort electron pulses. At pump intensities of 2.9 ∼ 7.1 × 1010 W cm−2, the transient electric fields last at least one nanosecond with a maximum field strength of 3.2 ∼ 5.3 × 104 V m−1 at 120 μm above the aluminum surface. The transient electric fields and the associated evolution of photoelectrons were explained by a ‘three-layer’ model. The potential influence of such fields on reflection ultrafast electron diffraction and time-resolved angle-resolved photoemission spectroscopy were evaluated.
Restoration of the Patient-Specific Anatomy of the Proximal and Distal Parts of the Humerus: Statistical Shape Modeling Versus Contralateral Registration Method

Background: In computer-assisted reconstructive surgeries, the contralateral anatomy is established as the best available reconstruction template. However, existing intra-individual bilateral differences or a pathological, contralateral humerus may limit the applicability of the method. The aim of the study was to evaluate whether a statistical shape model (SSM) has the potential to predict accurately the pretraumatic anatomy of the humerus from the posttraumatic condition. Methods: Three-dimensional (3D) triangular surface models were extracted from the computed tomographic data of 100 paired cadaveric humeri without a pathological condition. An SSM was constructed, encoding the characteristic shape variations among the individuals. To predict the patient-specific anatomy of the proximal (or distal) part of the humerus with the SSM, we generated segments of the humerus of predefined length excluding the part to predict. The proximal and distal humeral prediction (p-HP and d-HP) errors, defined as the deviation of the predicted (bone) model from the original (bone) model, were evaluated. For comparison with the state-of-the-art technique, i.e., the contralateral registration method, we used the same segments of the humerus to evaluate whether the SSM or the contralateral anatomy yields a more accurate reconstruction template. Results: The p-HP error (mean and standard deviation, 3.8° ± 1.9°) using 85% of the distal end of the humerus to predict the proximal humeral anatomy was significantly smaller (p = 0.001) compared with the contralateral registration method. The difference between the d-HP error (mean, 5.5° ± 2.9°), using 85% of the proximal part of the humerus to predict the distal humeral anatomy, and the contralateral registration method was not significant (p = 0.61). The restoration of the humeral length was not significantly different between the SSM and the contralateral registration method. Conclusions: SSMs accurately predict the patient-specific anatomy of the proximal and distal aspects of the humerus. The prediction errors of the SSM depend on the size of the healthy part of the humerus. Clinical Relevance: The prediction of the patient-specific anatomy of the humerus is of fundamental importance for computer-assisted reconstructive surgeries.