Miracle-dz/UniFAR-FTUs huggingface dataset:
Marine Cyanophages Demonstrate Biogeographic Patterns throughout the Global Ocean

ABSTRACT Myoviruses and podoviruses that infect cyanobacteria are the two major groups of marine cyanophages, but little is known of how their phylogenetic lineages are distributed in different habitats. In this study, we analyzed the phylogenetic relationships of cyanopodoviruses and cyanomyoviruses based on the existing genomes. The 28 cyanomyoviruses were classified into four clusters (I to IV), and 19 of the 20 cyanopodoviruses were classified into two clusters, MPP-A and MPP-B, with four subclusters within cluster MPP-B. These genomes were used to recruit cyanophage-like fragments from microbial and viral metagenomes to estimate the relative abundances of these cyanophage lineages. Our results showed that cyanopodoviruses and cyanomyoviruses are both abundant in various marine environments and that clusters MPP-B, II and III appear to be the most dominant lineages. Cyanopodoviruses and cluster I and IV cyanomyoviruses exhibited habitat-related variability in their relative levels of abundance, while cluster II and III cyanomyoviruses appeared to be consistently dominant in various habitats. Multivariate analyses showed that reads that mapped to Synechococcus phages and Prochlorococcus phages had distinct distribution patterns that were significantly correlated to those of Synechococcus and Prochlorococcus, respectively. The Mantel test also revealed a strong correlation between the community compositions of cyanophages and picocyanobacteria. Given that cyanomyoviruses tend to have a broad host range and some can cross-infect Synechococcus and Prochlorococcus, while cyanopodoviruses are commonly host specific, the observation that their community compositions both correlated significantly with that of picocyanobacteria was unexpected. Although cyanomyoviruses and cyanopodoviruses differ in host specificity, their biogeographic distributions are likely both constrained by the picocyanobacterial community.
Design and analysis of parallel algorithms

Kurskod: 5DV050 Inrättad: 2008-03-31 Inrättad av: teknisk-naturvetenskapliga fakultetsnämnden Reviderad: 2012-02-29 Reviderad av: teknisk-naturvetenskapliga fakultetsnämnden Kursplan giltig från: 2012, vecka 10 Ansvarig enhet: Inst för datavetenskap SCB-ämnesrubrik: Informatik/Dataoch systemvetenskap Huvudområden och successiv fördjupning: Beräkningsteknik: Avancerad nivå, har endast kurs/er på grundnivå som förkunskapskrav (A1N) , Datavetenskap: Avancerad nivå, har endast kurs/er på grundnivå som förkunskapskrav (A1N) Betygsskala: För denna kurs ges betygen 5 Med beröm godkänd, 4 Icke utan beröm godkänd, 3 Godkänd, VG Väl godkänd, G Godkänd, U Underkänd Utbildningsnivå: Avancerad nivå
Decitabine improves outcomes in older patients with acute myeloid leukemia and higher blast counts

The median age at diagnosis of patients with acute myeloid leukemia (AML) is 66 years, and most patients are > 60 years of age. [1] Due to comorbidities and adverse-risk disease, many older patients may not benefit from intensive chemotherapy. [2, 3] Hypomethylating agents such 5-azacytidine (AZA) and decitabine (DAC) have been used as “lower-intensity” therapy in older patients with AML and may be associated with outcomes similar to intensive therapy. [4, 5] In a post-hoc analysis of a randomized phase III trial of AZA vs. conventional care regimens (CCR) in patients with higher-risk myelodysplastic syndrome (MDS) and 20–30% blasts, AZA produced a response rate of 18% and was associated with an improvement in overall survival (OS) compared to CCR (24.5 vs. 16 months, p=0.001). [6] Subsequent reports have confirmed the activity of AZA in older patients with AML and in those unfit for intensive chemotherapy. [4, 7–9]
3D Boundary element meshing for multiscale bone anisotropic analysis

ABSTRACT Bone health conditions are treated with prosthesis and implant fixations. Despite being there to assist the patient, the difference between the elastic properties of these artificial medical solutions and the treated bone region may lead to a new fracture. One strategy to circumvent that problem, reducing the gap between the elastic properties, is to use Functionally Graded Materials in the manufacture of such medical devices. It is therefore of vital importance to understand the mechanical properties of bone within the region of interest, once this knowledge may ease and improve the development of artificial medical solutions. The bone tissue is a hierarchical material which has different elastic behaviour depending upon the scale of interest, the particular bone and the bone region. In this work, a multi-scale BEM mesh model of bone tissue ranging from the nanoscale to the mesoscale is sought. A new nanoscale design which considers the hydroxyapatite crystals inside, and outside the fibrils is developed. Furthermore, the fibrils are modelled with reported elliptical cross sections. Additionally, a procedure to develop the BEM meshes using multimedia software is proposed, based upon the similarities between them. Finally, several mesheswere created using triangular continuous elements.
MICROSCOPIC AND PHASE ANALYSIS OF CEMENT PASTE CONTAINING WASTE MICRONIZED MARBLE POWDER

The article focuses on the impact of waste marble powder on resulting cement composites. We investigate of influence waste marble powder on the hydration process and hence the resulting phase composition. The hydration process was investigated using calorimetry and phase composition of the resulting composite by electron microscopy. The results are compared with a reference sample composed of Portland cement.
Habitual emotion regulation strategies and baseline brain perfusion

Specific emotion regulation styles like the frequent use of expressive suppression and low capacity for cognitive reappraisal has been associated with poorer mental health and a risk for depressive symptoms. Using arterial spin labeling, we investigated the effects of these regulation styles on regional cerebral blood flow (rCBF) in healthy participants during rest. Suppression scores correlated with increased rCBF in the ventral medial prefrontal cortex. Blood flow in this region was associated with elevated rCBF in other areas involved in emotional appraisal and control, and may represent neurobiological correlates of increased habitual self-monitoring as common in depression and anxiety. By linking default brain functioning to emotional styles, we provide an insight into the neurobiology of the predisposition to depression.
Education and Default Incentives with Government Student Loan Programs

Electrically conductive polypyrrole and its derivatives are prepared by polymerizing compounds of the formula: (I) wherein R1, R2 and R3 are independently hydrogen, halogen, R4, -OR4 or -SR4; and R4 is aryl of 4 to 12 carbons or aliphatic of 1 to 20 carbons; comprising reacting the compound of formula I in the presence of an initiator, the initiator comprising a 2-substituted pyrrole nucleus which has a lower oxidation potential than the compound of formula I and which is capable of being incorporated into the polymer resulting from the polymerization reaction; a chemical oxidant or an applied electrochemical potential; and a solvent.
A reliable non-verbal vocal input metaphor for clicking

While experiencing an immersive virtual environment a suitable trigger metaphor is often needed, e.g. for the interaction with objects out of physical reach or system control. The BlowClick approach [35] that is based on non-verbal vocal input has been proven to be a valuable trigger technique in previous work. However, its original detection method is vulnerable to false positives and, thus, is limited in its potential use. Therefore, we extended the existing approach by adding machine learning methods to reliably classify blowing events. We found a support vector machine with Gaussian kernel performing the best with at least the same latency and more precision than before. Furthermore, we added acoustic feedback to the NVVI trigger, which increases the user's confidence and whose absence was also stated as a limitation of the previous work. With this extended technique, we repeated the conducted Fitts' law experiment with 33 participants and could confirm that it is possible to use NVVI as a reliable trigger as part of a hands-free point-and-click interface. Furthermore, we tested reaction times to measure the trigger's performance without the influence of pointing and calculated device throughputs to ensure comparability.
On-line spectral estimation of nonstationary time series based on AR model parameter estimation and order selection with a forgetting factor

A new method for on-line spectral estimation of nonstationary time series via autoregressive (AR) model construction is proposed. The method consists of on-line parameter estimation based on the recursive least squares ladder estimation algorithm with a forgetting factor and on-line order determination based on AIC with some modifications. The effectiveness of the proposed method is demonstrated by computer simulation study and applying to the actual data of electroencephalogram (EEG). >
Universal Admission Screening for Methicillin-Resistant Staphylococcus aureus in a Level HID Neonatal Intensive Care Unit: The First 9 Months

In response to epidemic methicillin-resistant Staphylococcus aureus (MRSA) in the community, the Illinois General Assembly mandated that all patients admitted to intensive care units statewide be screened for MRSA. Screening was instituted at our neonatal intensive care unit (NICU) in September 2007 by a polymerase chain reaction (PCR)-based strategy. The law created an opportunity to determine the rate of MRSA colonization among neonates, to gather information about subsequent MRSA infections, and to evaluate risk factors for MRSA colonization on admission to the NICU.
Pitch-sensitive Components Emerge from Hierarchical Sparse Coding of Natural Sounds

The neural basis of pitch perception, our subjective sense of the tone of a sound, has been a great ongoing debates in neuroscience.Variants of the two classic theories spectral Place theory and temporal Timing theory continue to continue to drive new experiments and debates (Shamma, 2004). Here we approach the question of pitch by applying a theoretical model based on the statistics of natural sounds. Motivated by gist research (Oliva and Torralba, 2006), we extended the nonlinear hierarchical generative model developed by Karklin et al. (Karklin and Lewicki, 2003) with a parallel gist pathway. The basic model encodes higher-order structure in natural sounds capturing variations in the underlying probability distribution. The secondary pathway provides a fast biasing of the model’s inference process based on the coarse spectrotemporal structures of sound stimuli on broader timescales. Adapting our extended model to speech demonstrates that the learned code describes a more detailed and broader range of statistical regularities that reflect abstract properties of sound such as harmonics and pitch than models without the gist pathway. The spectrotemporal modulation characteristics of the learned code are better matched to the modulation spectrum of speech signals than alternate models, and its higher-level coefficients capture information which not only effectively cluster related speech signals but also describe smooth transitions over time, encoding the temporal structure of speech signals. Finally, we find that the model produces a type of pitch-related density components which combine temporal and spectral
Sixty Years (1957–2017) of Research on Toxoplasmosis in China—An Overview

Toxoplasma gondii is a ubiquitous zoonotic pathogen belonging to apicomplexan parasites. Infection in humans and animals may cause abortion and other severe symptoms under certain circumstances, leading to great economical losses and public health problems. T. gondii was first discovered in China in 1955 and the corresponding work was published in 1957. Since then, a lot of work has been done on this parasite and the diseases it causes. This review summarizes the major progress made by Chinese scientists over the last 60 years, and gives our perspectives on what should be done in the near future. A wide variety of diagnostic approaches were designed, including the ones to detect T. gondii specific antibodies in host sera, and T. gondii specific antigens or DNA in tissue and environmental samples. Further work will be needed to translate some of the laboratory assays into reliable products for clinic uses. Epidemiological studies were extensively done in China and the sero-prevalence in humans increased over the years, but is still below the world average, likely due to the unique eating and cooking habits. Infection rates were shown to be fairly high in meat producing animals such as, pigs, sheep, and chickens, as well as in the definitive host cats. Numerous subunit vaccines in the form of recombinant proteins or DNA vaccines were developed, but none of them is satisfactory in the current form. Live attenuated parasites using genetically modified strains may be a better option for vaccine design. The strains isolated from China are dominated by the ToxoDB #9 genotype, but it likely contains multiple subtypes since different ToxoDB #9 strains exhibited phenotypic differences. Further studies are needed to understand the general biology, as well as the unique features of strains prevalent in China.
Mental Juggling: When Does Multitasking Impair Reading Comprehension?

ABSTRACT The present study investigated the conditions under which multitasking impairs reading comprehension. Participants read prose passages (the primary task), some of which required them to perform a secondary task. In Experiment 1, we compared two different types of secondary tasks (answering trivia questions and solving math problems). Reading comprehension was assessed using a multiple-choice test that measured both factual and conceptual knowledge. The results showed no observable detrimental effects associated with multitasking. In Experiment 2, the secondary task was a cognitive load task that required participants to remember a string of numbers while reading the passages. Performance on the reading comprehension test was lower in the cognitive load conditions relative to the no-load condition. The present study delineates the conditions under which multitasking can impair or have no effect on reading comprehension. These results further our understanding of our capacity to multitask and have practical implications in our technologically advanced society in which multitasking has become commonplace.
Maternal residence near municipal waste incinerators and the risk of urinary tract birth defects

Objectives Waste incineration releases a mixture of chemicals with high embryotoxic potential, including heavy metals and dioxins/furans, into the atmosphere. In a previous ecological study we found an association between the risk of urinary tract birth defects and residence in the vicinity of municipal solid waste incinerators (MSWIs). The objective of the present study was to specifically test this association. Methods A population-based case–control study compared 304 infants with urinary tract birth defects diagnosed in the Rhône-Alpes region (2001–2003) with a random sample of 226 population controls frequency-matched for infant sex and year and district of birth. Exposure to dioxins in early pregnancy at the place of residence, used as a tracer of the mixture released by 21 active waste incinerators, was predicted with second-generation Gaussian modelling (ADMS3 software). Other industrial emissions of dioxins, population density and neighbourhood deprivation were also assessed. Individual risk factors including consumption of local food were obtained by interviews with 62% of the case and all control families. Results Risk was increased for mothers exposed to dioxins above the median at the beginning of pregnancy (OR 2.95, 95% CI 1.47 to 5.92 for dioxin deposits). When only interviewed cases were considered, risk estimates decreased mainly because the non-interviewed cases were more likely to live in exposed residential environments (OR 2.05, 95% CI 0.92 to 4.57). The results suggest that consumption of local food modifies this risk. Conclusions This study confirms our previous observation of a link between the risk of urinary tract birth defects and exposure to MSWI emissions in early pregnancy and illustrates the effect of participation bias on risk estimates of environmental health impacts.
Atypical Glandular Cells on Cervical Cytology and Breast Disease: What Is the Association?

Objective. To determine whether metastatic mammary carcinoma can be detected on cervical cytology in patients with atypical glandular cells (AGCs). Methods. This blinded study of AGC cases with a matched control group was approved by Hartford Hospital institutional review board. Between January 2002 and November 2008, inclusive, all Pap tests in our database with AGC were identified. The AGC cases from patients with breast disease, compared with the control group of AGC patients without breast disease, were reanalyzed independently by 2 pathologists. Results. Among the 40 women who had an AGC Pap test with breast disease, 21 cases were available for review (16 with invasive and 5 with in situ breast lesions). Seventeen cases of AGC in patients without breast disease served as the control group. The 2 pathologists agreed with the original Pap finding (AGC) in 84.2% to 89.5% of cases. There were no cases, either among those with breast disease or those without, where cells consistent with breast disease were seen, nor were "tamoxifen cells" identified, on Pap testing. Conclusions. Studies have found that an association exists between patients with AGCs on cervical cytology and extrauterine malignancies, including breast disease. The results of this analysis would suggest that, at least for breast disease, the higher association of cancer or precancerous lesions in those with AGC is not related to the direct extension of disease or metastasis. Further research will be needed to help delineate the potential etiology of this association.
Delivery system integration and health care spending and quality for Medicare beneficiaries.

IMPORTANCE The Medicare accountable care organization (ACO) programs rely on delivery system integration and health care provider risk sharing to lower spending while improving quality of care. OBJECTIVE To compare spending and quality between larger and smaller provider groups and examine how size-related differences vary by 2 factors considered central to ACO performance: group primary care orientation and financial risk sharing by health care providers. EVIDENCE REVIEW Using 2009 Medicare claims and linked American Medical Association Group Practice data, we assigned 4.29 million beneficiaries to health care provider groups based on primary care use. We categorized group size according to eligibility thresholds for the Shared Savings (≥5000 assigned beneficiaries) and Pioneer (≥15,000) ACO programs and distinguished hospital-based from independent groups. We assessed the primary care orientation of larger groups' specialty mix and used health maintenance organization market penetration and data from the Community Tracking Study to measure the extent of financial risk accepted by different types of provider groups in different areas for managed care patients. We estimated linear regression models comparing spending and quality between larger and smaller health care provider groups, allowing size-related differences to vary by measures of group primary care orientation and risk sharing. Spending and quality measures included total medical spending, spending by type of service, 5 process measures of quality, and 30-day readmissions, all adjusted for sociodemographic and clinical characteristics. FINDINGS Compared with smaller groups, larger hospital-based groups had higher total per-beneficiary spending in 2009 (mean difference, +$849), higher 30-day readmission rates (+1.3 percentage points), and similar performance on 4 of 5 process measures of quality. In contrast, larger independent physician groups performed better than smaller groups on all process measures and exhibited significantly lower per-beneficiary spending in counties where risk sharing by these groups was more common (-$426). Among all groups sufficiently large to participate in ACO programs, a strong primary care orientation was associated with lower spending, fewer readmissions, and better quality of diabetes care. CONCLUSIONS AND RELEVANCE Spending was lower and quality of care better for Medicare beneficiaries served by larger independent physician groups with strong primary care orientations in environments where health care providers accepted greater risk.
TLR4-Dependent Immune Response Promotes Radiation-Induced Liver Disease by Changing the Liver Tissue Interstitial Microenvironment during Liver Cancer Radiotherapy

Liver tissue interstitial fluid (TIF) a special microenvironment around liver cells, which may play a vital role in cell communication during liver injury. Moreover, toll-like receptor 4 (TLR4) is an important trigger of the immune response that may also play a role in liver injuries, including radiation-induced liver disease (RILD). Therefore, the purpose of this study was to identify the roles of the TLR4-dependent immune response and TIFs in RILD after radiation therapy (RT) for liver cancer. This study consisted of two phases, and in the primary phase, the livers of TLR4 mutant (TLR4–) and normal (TLR4+) mice were irradiated with 30 Gy. TIF was then obtained from mouse livers and assessed by cytokine array analysis 20 days after irradiation, and cytokines in the TIFs, TLR4 and RILD were analyzed. In the second or validation phase, hepatocytes were isolated from TLR4+ or TLR4– mice irradiated with 8 Gy and were co-cultured with TIFs from mouse livers, apoptosis of the hepatocytes was then measured using flow cytometry. We found that severe RILD was accompanied by higher expression of granulocyte macrophage colony-stimulating factor (GM-CSF), tumor necrosis factor-related apoptosis inducing ligand (TRAIL) and vascular endothelial growth factor receptor 2(VEGFR-2) in liver TIFs, from in TLR4+ mice compared with TLR4– mice (P < 0.05). In both TLR4+ and TLR4– hepatocytes, apoptosis after irradiaton was increased significantly after co-culture in TIFs from TLR4+ mice that had their livers irradiated, compared with TIFs from TLR4– mice that had their livers irradiated or TIFs from unirradiated mice (P < 0.05). In summary, these findings indicate that the TLR4-dependent immune response may promote RILD by enhancing the expression of GM-CSF, VEGFR-2 and TRAIL in liver TIFs.
Downgrade Resilience in Key-Exchange Protocols

Key-exchange protocols such as TLS, SSH, IPsec, and ZRTP are highly configurable, with typical deployments supporting multiple protocol versions, cryptographic algorithms and parameters. In the first messages of the protocol, the peers negotiate one specific combination: the protocol mode, based on their local configurations. With few notable exceptions, most cryptographic analyses of configurable protocols consider a single mode at a time. In contrast, downgrade attacks, where a network adversary forces peers to use a mode weaker than the one they would normally negotiate, are a recurrent problem in practice. How to support configurability while at the same time guaranteeing the preferred mode is negotiated? We set to answer this question by designing a formal framework to study downgrade resilience and its relation to other security properties of key-exchange protocols. First, we study the causes of downgrade attacks by dissecting and classifying known and novel attacks against widely used protocols. Second, we survey what is known about the downgrade resilience of existing standards. Third, we combine these findings to define downgrade security, and analyze the conditions under which several protocols achieve it. Finally, we discuss patterns that guarantee downgrade security by design, and explain how to use them to strengthen the security of existing protocols, including a newly proposed draft of TLS 1.3.