Miracle-dz/UniFAR-FTUs huggingface dataset:
Using quantitative features extracted from T2-weighted MRI to improve breast MRI computer-aided diagnosis (CAD)

Computer-aided diagnosis (CAD) has been proposed for breast MRI as a tool to standardize evaluation, to automate time-consuming analysis, and to aid the diagnostic decision process by radiologists. T2w MRI findings are diagnostically complementary to T1w DCE-MRI findings in the breast and prior research showed that measuring the T2w intensity of a lesion relative to a tissue of reference improves diagnostic accuracy. The diagnostic value of this information in CAD has not been yet quantified. This study proposes an automatic method of assessing relative T2w lesion intensity without the need to select a reference region. We also evaluate the effect of adding this feature to other T2w and T1w image features in the predictive performance of a breast lesion classifier for differential diagnosis of benign and malignant lesions. An automated feature of relative T2w lesion intensity was developed using a quantitative regression model. The diagnostic performance of the proposed feature in addition to T2w texture was compared to the performance of a conventional breast MRI CAD system based on T1w DCE-MRI features alone. The added contribution of T2w features to more conventional T1w-based features was investigated using classification rules extracted from the lesion classifier. After institutional review board approval that waived informed consent, we identified 627 breast lesions (245 malignant, 382 benign) diagnosed after undergoing breast MRI at our institution between 2007 and 2014. An increase in diagnostic performance in terms of area under the curve (AUC) from the receiver operating characteristic (ROC) analysis was observed with the additional T2w features and the proposed quantitative feature of relative T2w lesion intensity. AUC increased from 0.80 to 0.83 and this difference was statistically significant (adjusted p-value = 0.020).
The new species Brucella microti replicates in macrophages and causes death in murine models of infection.

BACKGROUND The recent isolation of Brucella microti from the common vole, the red fox, and the soil raises the possibility of an eventual reemergence of brucellosis in Europe. In this work, the pathogenic potential of this new Brucella species in both in vitro and in vivo models of infection was analyzed. METHODS The ability of B. microti (as compared to that of the closely related species Brucella suis) to replicate in human macrophages and in human and murine macrophage-like cells was determined. The behavior of B. microti and B. suis was evaluated in vivo in murine models of infection with Balb/c, CD1, and C57BL/6 mice. RESULTS B. microti showed an enhanced capacity for intramacrophagic replication compared with that of B. suis. Surprisingly, and in contrast to other species of Brucella, 10(5) colony-forming units of B. microti killed 82% of Balb/c mice within 7 days. Infection of spleen and liver with B. microti peaked at day 3, compared with B. suis infection, which peaked at day 7. Sublethal doses of B. microti induced good protection against a subsequent challenge with lethal doses. CONCLUSIONS In experimental cellular and murine infections, B. microti exhibited a high pathogenic potential, compared with other Brucella species.
Pyrophosphate in Synovial Fluid and Urine and its Relationship to Urinary Risk Factors for Stone Disease

Inorganic pyrophosphate (PPi) measurement in urine and synovial fluid has been established using the PPi-dependent phosphorylation of fructose-6-phosphate and subsequent reduction of dihydroxyacetone phosphate by NADH. The assay is linear up to 200 μmol/L, easy to perform and gives results comparable to more complex methods. Daily urinary output of PPi was independently related to both age (P = 0·0014) and sex (P = 0·0002). Men had higher values than women and older individuals excreted greater amounts. Male stone formers, younger than 45 years, had lower values than age matched male controls (P = 0·012). Younger female stone formers also tended to have lower values. In stone formers' urine significant and independent correlations were found of PPi excretion with urine volume (P = 0·004) and with phosphate excretion (P = 0·008). Oxalate excretion and that of other urine constituents and the degree of supersaturation with common stone-forming salts were not correlated with PPi. PPi excretion was markedly elevated in the urine of two patients with hypophosphatasia. The PPi concentration in synovial fluid from painful, swollen knee joints was elevated, but unrelated to the presence or absence of PPi or urate crystals.
The Younger Dryas in the English Lake District: reconciling geomorphological evidence with numerical model outputs

The geomorphology of the south‐western and central Lake District, England is used to reconstruct the mountain palaeoglaciology pertaining to the Lateglacial and Younger Dryas. Limitations to previous ice‐mass reconstructions and consequent palaeoclimatic inferences include: (i) the use of static (steady‐state) glacier reconstructions, (ii) the assumption of a single‐stage Younger Dryas advance, (iii) greatly varying ice‐volume estimates, (iv) inexplicable spatial variations in ELA (Equilibrium Line Altitude), and (v) a lack of robust extent chronology. Here we present geomorphological mapping based on aerial photography and the NextMap Britain Digital Elevation Model, checked by ground survey. Former glacier extents were inferred and ELAs were calculated using the Balance Ratio method of Osmaston. Independently, a time‐dependant 2‐D ice‐flow model was forced by a regional ELA history that was scaled to the GRIP record. This provided a dynamic reconstruction of a mountain ice field that allowed for non‐steady‐state glacier evolution. Fluctuations in climate during the Younger Dryas resulted in multiple glacial advance positions that show agreement with the location of mapped moraines, and may further explain some of the ELA variations found in previous local and static reconstructions. Modelling based on the GRIP record predicts three phases: an initial maximum extent, a middle minor advance or stillstand, and a pronounced but less extensive final advance. The comparisons find that the reconstructions derived from geomorphological evidence are effective representations of steady‐state glacier geometries, but we do propose different extents for some glaciers and, in particular, a large former glacier in Upper Eskdale.
Observation of swell dissipation across oceans

Global observations of ocean swell, from satellite Synthetic Aperture Radar data, are used to estimate the dissipation of swell energy for a number of storms. Swells can be very persistent with energy e‐folding scales exceeding 20,000 km. For increasing swell steepness this scale shrinks systematically, down to 2800 km for the steepest observed swells, revealing a significant loss of swell energy. This value corresponds to a normalized energy decay in time β = 4.2 × 10−6 s −1. Many processes may be responsible for this dissipation. The increase of dissipation rate in dissipation with swell steepness is interpreted as a laminar to turbulent transition of the boundary layer, with a threshold Reynolds number of the order of 100,000. These observations of swell evolution open the way for more accurate wave forecasting models, and provide a constraint on swell‐induced air‐sea fluxes of momentum and energy.
Specification and prediction of nickel mobilization using artificial intelligence methods

Groundwater and soil pollution from pyrite oxidation, acid mine drainage generation, and release and transport of toxic metals are common environmental problems associated with the mining industry. Nickel is one toxic metal considered to be a key pollutant in some mining setting; to date, its formation mechanism has not yet been fully evaluated. The goals of this study are 1) to describe the process of nickel mobilization in waste dumps by introducing a novel conceptual model, and 2) to predict nickel concentration using two algorithms, namely the support vector machine (SVM) and the general regression neural network (GRNN). The results obtained from this study have shown that considerable amount of nickel concentration can be arrived into the water flow system during the oxidation of pyrite and subsequent Acid Drainage (AMD) generation. It was concluded that pyrite, water, and oxygen are the most important factors for nickel pollution generation while pH condition, SO4, HCO3, TDS, EC, Mg, Fe, Zn, and Cu are measured quantities playing significant role in nickel mobilization. SVM and GRNN have predicted nickel concentration with a high degree of accuracy. Hence, SVM and GRNN can be considered as appropriate tools for environmental risk assessment.
Daily and Circadian Rhythms of Tissue Factor Pathway Inhibitor and Factor VII Activity

Objective—Diurnal variations in levels of factor VII (FVII), FVIII, proteins C and S, antithrombin, plasminogen activator inhibitor-1, prothrombin fragment F1+2, and D-dimers in healthy humans point to the existence of circadian rhythms of coagulation factors. We sought for temporal fluctuations of tissue factor pathway inhibitor (TFPI) activity in human and mouse plasma. Methods and Results—TFPI activity showed significant daily variations with highest levels in the morning in healthy men (+11%) and in mice at the light-to-dark transition (+63%), the beginning of the physically active period. Variations in FVII activity paralleled those in TFPI. In mice, the feeding schedule had a strong impact on these rhythms. Although restricted feeding and fasting shifted the peak of TFPI, the FVII peak disappeared. Investigation of temporal fluctuations in constant darkness indicated the existence of daily rhythms for TFPI and of true circadian rhythms for FVII. Conclusions—For the first time, we report, both in humans and mice, temporal variations in TFPI activity. The coherent variations in FVII and TFPI activity could interplay to maintain the coagulation equilibrium. The chronobiological patterns should be considered to analyze activity levels of these factors. Moreover, the mouse model could be exploited to investigate modifiers of coagulation rhythms potentially associated to morning peaks of cardiovascular events.
Metaphoric identity mapping: Facilitating goal setting and engagement in rehabilitation after traumatic brain injury

Difficulty re-establishing an organised and compelling sense of personal identity has increasingly been identified as a critical theme in outcome studies of individuals with severe traumatic brain injury (TBI) and a serious obstacle to active engagement in rehabilitation. There exists little empirical support for approaches to identity reconstruction that address common impairments associated with TBI. Similarly, there is as yet little empirical support for theoretically sound approaches to promoting engagement in goal setting for this population. This article has two purposes. First, theory and procedures associated with metaphoric identity mapping are discussed in relation to goal setting in TBI rehabilitation. Second, the results of a qualitative pilot study are presented. The study explored metaphoric identity mapping as a facilitator of personally meaningful goal setting with five individuals with significant disability many years after their injury. Drawing on principles of grounded theory, the investigators extracted data from semi-structured interviews with clients and clinicians, from focus groups with the clinicians, and from observation of client–clinician interaction. Analysis of the data yielded five general themes concerning the use of this approach: All clients and clinicians found identity mapping to be an acceptable process and also useful for deriving meaningful rehabilitation goals. Both clients and clinicians saw client-centred goals as important. Cognitive impairments posed obstacles to this goal-setting intervention and mandated creative compensations. And finally, identity-related goal setting appeared to require a “mind shift” for some clinicians and demanded clinical skills not uniformly distributed among rehabilitation professionals.
Dynamic Changes of the Phosphoproteome in Postmortem Mouse Brains

Protein phosphorylation is deeply involved in the pathological mechanism of various neurodegenerative disorders. However, in human pathological samples, phosphorylation can be modified during preservation by postmortem factors such as time and temperature. Postmortem changes may also differ among proteins. Unfortunately, there is no comprehensive database that could support the analysis of protein phosphorylation in human brain samples from the standpoint of postmortem changes. As a first step toward addressing the issue, we performed phosphoproteome analysis with brain tissue dissected from mouse bodies preserved under different conditions. Quantitative whole proteome mass analysis showed surprisingly diverse postmortem changes in phosphoproteins that were dependent on temperature, time and protein species. Twelve hrs postmortem was a critical time point for preservation at room temperature. At 4°C, after the body was cooled down, most phosphoproteins were stable for 72 hrs. At either temperature, increase greater than 2-fold was exceptional during this interval. We found several standard proteins by which we can calculate the postmortem time at room temperature. The information obtained in this study will be indispensable for evaluating experimental data with human as well as mouse brain samples.
In-silico analysis of MHC genes in hereditary colorectal cancer shows identical by state SNP sharing affecting HLA-DQB1 binding groove

Background The role of Human Leukocyte Antigen (HLA) alleles in colorectal cancer susceptibility, development and progression is the focus of ongoing scrutiny. MHC polymorphisms in a Sudanese family with hereditary colorectal cancer were studied using an in silico approach and the results were verified using The Cancer Genome Atlas (TCGA). In this family study, we tested for sharing of nucleotide polymorphisms identified by whole exome capture in major histocompatibility complex region and carried out in-silico prediction of their effects in tumor and control samples. SNPs were analyzed to highlight identical by state sharing, to identify runs of homozygosity, as well as to predict structural and functional effects using homology modeling, damaging effect predictions, and regulatory changes prediction. Results MHC II area showed significantly high degree of homozygosity in tumor samples. Non-synonymous SNPs shared identical by state (IBS) between tumor samples were predicted to affect HLA-DQB1 binding groove. A similar haplotype of these SNPs was identified in a TCGA colonic adenocarcinoma tumor sample. No significant regulatory effects (in the form of transcription factor or miRNA binding site variants) were predicted. Conclusions The results demonstrate IBS SNP sharing of markers affecting HLA-DQB1 binding specificity and probable loss of heterozygosity in MHC II region in colorectal cancer. The significance of this sharing in cancer pathogenesis remains to be established.
Initial growth responses to controlled release fertilizer application at establishment of commercial forestry species in South Africa

In South Africa fertilizer applications at establishment is a common practice in the forestry industry. Recommendations are based on past research with conventional sources (CV) and as a result there have only been slight improvements in additional plantation production over recent years. The objective of this study was to investigate initial stand responses in terms of leaf are index (LAI), foliar nutrient content, biomass index (BI) and volume growth to the application of controlled release fertilizers (CRF) at re-establishment. Nitrogen (N), phosphorus (P) and potassium (K) were applied in a three way factorial combination to Pinus radiata at planting on a site in the Western Cape. The design was replicated five times across the study area. N (CRF) and P (CV) were applied in a two way factorial combination at planting to two Eucalyptus grandis x urophylla hybrids and Eucalyptus dunnii across three sites, one exagricultural and two re-establishment sites, on the Zululand coastal plain and the Midlands region. The design was replicated nine times on each study site. Harvesting residues were burnt on the eucalypt sites prior to establishment and may have had an impact on the responses found. An outbreak of Fusarium circinatum on the P. radiata site resulted in unexpected and extremely variable responses. An attempt to quantify the effect of the disease had limited success. The mean BI of the control treatment reached 25. The best CV and CRF treatments yielded improvements of 42 % and 83 % in BI over the control respectively, with only the CRF treatment difference being significant. Foliar analysis results revealed marginal to deficient concentrations of P and Mg being alleviated by the treatments in question. On the KZN Zululand sites there was a marked response of the hybrids to N with P having an additive effect on volume growth, LAI and foliar N content. Application of 120 g N and 20 g P per tree on the ex-agriculture site produced a volume of 8 m ha at one year of age, a significant increase of 118 % and 80 % over the control and best CV treatment respectively. Application of 80 g N and 20 g P per tree, on the reestablishment site, yielded a volume of 24.6 m ha at one year which equates to a significant 39 % and insignificant 7 % additional volume at one year over the control and best CV treatment respectively. A non-significant suppressive effect was found with 20 g CV P application only. Stellenbosch University http://scholar.sun.ac.za
The effect of cluster ions on anomalous VHF backscatter from the summer polar mesosphere

Radar backscatter at 50 MHz from the summer polar mesosphere is sometimes much stronger than the scatter from other latitudes at any time or from polar latitudes in other seasons. Kelley and Ulwick [1987] suggested that heavy water cluster ions in this uniquely cold region of the atmosphere could be responsible because, in the presence of these ions, the enhanced, turbulence-driven spectrum of the ionization irregularities could extend to considerably shorter wavelengths than that of the neutral turbulence itself. Here we explore this idea further and relate it to past and planned incoherent scatter measurements at EISCAT. These observations should be able to establish whether or not water cluster ions have an anomalously low diffusion coefficient.
A LiFePO4 battery discharge simulator for EV applications — Part 2: Developing the battery simulator

This paper, the second of the series on developing a LiFePO4 (LFP) battery discharge simulator for EV applications, presents an approach for developing the battery simulator. After the optimal battery model was established, in the first paper, the main drawbacks of battery simulator are addressed and a new strategy is proposed. This strategy uses neural networks (NN) for online estimation of the battery parameters during discharge. The proposed simulator is validated by comparisons with a typical simulator and data from a LFP battery submitted to discharge profile in concordance with a driving cycle.
Photoperiodic Flowering Response of Biloxi Soybean in 72-Hour Cycles.

Recently, evidence has accumulated to indicate that the photoperiodic control of floral induction is mediated by an endogenous rhythm with periods of approximately 24 hours (9, 10, 11, 12, 13, 18, 19, 20, 21,22). It has long been known that the floral response of Biloxi soybean varies with the length of the photoperiod (4, 5, 6, 7,18). The optimum response with 24-hour treatment cycles is obtained with photoperiods between 6 and 10 hours and normally no flowering is produced with photoperiods longer than 14 or perhaps 14Y2 hours (1, 28). Hamner (18), however, has shown that if a dark period of 16 hours is given in each cycle after photoperiods of different lengths, flowering is obtained with photoperiods as long as 16 and 18 hours. In those experiments, however, the cycle duration was varied with the different lengths of photoperiods given. Since Nanda and Hamner (23) have demonstrated a periodic variation in floral response as a function of cycle durations, it was difficult to predict what results might be obtained with various photoperiods given in long cycles of standard duration. In the following experiments a 72-hour, or tridiurnal, cycle was used to further assess the effects of light breaks and differential photoperiod durations on photoperiodic and rhythmic flowering responses.
Local Spread and Lymph Node Involvement in Cervical Cancer

In 150 cases of carcinoma of the cervix the specimens obtained by radical hysterectomy and lymphadenectomy were examined by means of giant frontal section preparations which included adjacent parametria. Serial step sections of lymph nodes were performed. There were 44 cases of Stage IB, 13 of Stage 11 A, and 93 of Stage IIB. Lymph node involvement was 16%, 33%, and 37%, respectively. The size of each cervical tumor was expressed in square millimeters as an “area-equivalent,” the product of its vertical and horizontal diameters in the frontal plane. Cross relationships of tumor size, incidence of lymph node metastasis, border zone spread, and parametrial involvement were studied and are discussed. It is concluded that tumor size gives a better indication of tumor behavior than does clinical staging and constitutes an objective method of classifying tumors that the latter cannot attain.
Effect of a 9-Wk. after-School Multiskills Club on Fundamental Movement Skill Proficiency in 8- to 9-Yr.-Old Children: An Exploratory Trial

This exploratory study examined the effects of a 9-wk. after-school multiskills club on fundamental movement skill proficiency in 8- to 9-yr. -old children. Two schools were randomly assigned to either a control (n = 15 children) or multiskill club (n = 19 children) condition. The multiskill club received 18 coaching sessions designed to improve fundamental movement skills. The control group followed normal routines. 7 skills were assessed using process-oriented measures with video analysis. Participation in the multiskill club yielded significant improvements in proficiency at posttest only in static balance, while potentially practically important improvements were observed in performance of the catch, throw, and kick skills. The after-school multiskill club offered a viable opportunity for movement skill acquisition, but any such programme would need to run for a longer duration to assess whether this type of activity could benefit all skills.
Geology and U–Pb geochronology of the Espedalen Complex, southern Norway, and its position in the Caledonian nappe systems

Abstract The Espedalen Nappe is located in the east of the Jotun–Valdres Nappe Complex in southern Norway. Its main component, the Espedalen Complex, consists of an early suite of jotunite, charnockite and augengneiss, a main anorthosite–ultramafite–norite suite, and a late gabbronorite suite. Mafic dykes and lamprophyres cut the complex, some being feeders to the Stylskampen mafic to felsic suite at the western margin of the complex. The complex hosts Ni–Cu mineralizations which were mined in past centuries. Two crystalline outliers occur at Ormtjernkampen and Røssjøkollen further south. Caledonian convergence thrust the nappe on to Early Palaeozoic sedimentary rocks. Rocks of the Espedalen Complex are covered and/or tectonically interleaved with Late Precambrian conglomerates and arkoses of the Valdres Group. Dating of zircon and titanite by ID-TIMS U–Pb indicates formation of the complex at 1520–1510 Ma, followed by deformation and metamorphism between 1050 and 950 Ma during the Sveconorwegian orogeny, before the eventual translation during the Caledonian orogeny. These data indicate an affinity of the nappe with Telemarkian crust in the autochthonous Baltic basement, in contrast to the rocks of the overlying Jotun Complex which correlate instead to Gothian crust formed between 1600 and 1700 Ma.