Miracle-dz/UniFAR-FTUs huggingface dataset:
Differentiating benign from malignant solid breast masses with US strain imaging.

PURPOSE To prospectively evaluate the sensitivity and specificity of ultrasonographic (US) strain imaging for distinguishing between benign and malignant solid breast masses, with biopsy results as the reference standard. MATERIALS AND METHODS The study was institutional review board approved and HIPAA compliant. Informed consent was obtained from all participating patients. US strain imaging of 403 breast masses was performed. The 50 malignant and 48 benign lesions (in patients aged 19-83 years; mean age, 49 years +/- 17 [standard deviation]) with the highest quality were selected for the reader study. Three observers blinded to the pathologic outcomes first described the B-mode image findings by using US Breast Imaging Reporting and Data System descriptors and derived a probability of malignancy. They then updated the probability by assessing strain images. Receiver operating characteristic (ROC) curves were constructed by using these probabilities. Areas under the ROC curve, sensitivities, and specificities were calculated and compared. Interobserver variability and the correlation between automated and subjective image quality assessment were analyzed. RESULTS The average area under the ROC curve for all three readers after US strain imaging (0.903) was greater than that after B-mode US alone (0.876, P = .014). With use of a 2% probability of malignancy threshold, strain imaging-as compared with B-mode US alone-had improved average specificity (0.257 vs 0.132, P < .001) and high sensitivity (0.993 vs 0.987, P > .99). Significant interobserver variability was observed (P < .001). The ability to assess strain image quality appeared to correlate with the highest observer performance. CONCLUSION US strain imaging can facilitate improved classification of benign and malignant breast masses. However, interobserver variability and image quality influence observer performance.
The tolerability of transcranial electrical stimulation used across extended periods in a naturalistic context by healthy individuals

Transcranial electrical stimulation (tES) is one of the most widely implemented forms of non-invasive neuromodulation in basic and clinical neuroscience. Further, the use of tES by healthy populations for various purposes is growing widespread daily. The effects of tES protocols on the skin and other tissues has remained uncharacterized when used across extended periods of time by healthy individuals. Therefore, we examined the basic safety and tolerability profile of two distinct tES protocols used repeatedly across an extended period of time by healthy subjects and report our findings here for the first time. The safety and tolerability profile previously accumulated regarding extended use of tES in clinical populations is compelling and supports a low-risk or non-significant risk designation. In the present study, we tested the tolerability (safety) and compliance, compared to sham, of two common tES approaches having a current density < 2 mA/cm2; transcranial Direct Current Stimulation (tDCS) or transcranial Pulsed Current Stimulation (tPCS) used by healthy subjects three to five days (17 20 minutes per day) per week for up to six weeks in a naturalistic environment. In this study 100 healthy subjects were randomized to one of three treatment groups: tDCS (n = 33), tPCS (n = 30), or sham (n = 37) and blinded to the treatment condition. The tES and sham waveforms were delivered through selfadhering electrodes on the right lateral forehead and back of the neck. We conducted 1905 treatment sessions (636 sham, 623 tDCS, and 646 tPCS sessions) on study volunteers over a six-week period. There were no serious adverse events in any treatment condition. Common side effects were primarily restricted to influences upon the skin and included skin tingling, itching, and mild burning sensations. The incidence of these events in active tES treatment arms (tPCS, tDCS) was equivalent or significantly lower than their incidence in the sham treatment arm. Other adverse events had a rarity (< 5% incidence) that could not be statistically distinguished across the treatment groups. Some subjects withdrew early from the study for atypical headache (sham n = 2, tDCS n = 2, and tPCS n = 3), atypical discomfort (sham n = 0, tDCS n = 1, and tPCS n = 1), or atypical skin irritation (sham n = 2, tDCS n = 8, and tPCS n = 1). The compliance (elected sessions completed) for tPCS was significantly greater when compared to sham (p = 0.007). The present study represents the most comprehensive analysis of tES tolerability and safety in healthy subjects to date. Limited to the hardware, electrodes, and protocols tested here, we conclude that repeated use of limited output tES across extended periods, is well tolerated and poses no significant risks to healthy subjects, as previously observed in clinical studies.
The First Measurement of Cassiopeia A’s Forward Shock Expansion Rate

We have obtained a second-epoch observation of the Cassiopeia A supernova remnant (SNR) with the Chandra X-Ray Observatory to measure detailed X-ray proper motions for the first time. Both observations are 50 ks exposures of the ACIS-S3 chip, and they are separated by 2 years. Measurements of the thin X-ray continuum-dominated filaments located around the edge of the remnant (which are identified with the forward shock) show expansion rates from 0.02% to 0.33% yr-1. Many of these filaments are therefore significantly decelerated. Their median value of 0.21% yr-1 is equal to the median expansion of the bright ring (0.21% yr-1) as measured with Einstein and ROSAT. This presents a conundrum if the motion of the bright ring is indicative of the reverse shock speed. We have also reevaluated the motion of the radio bright ring with emphasis on angle-averaged emissivity profiles. Our new measurement of the expansion of the angle-averaged radio bright ring is 0.07% ± 0.03% yr-1, somewhat slower than the previous radio measurements of 0.11% yr-1, which were sensitive to the motions of small-scale features. We propose that the expansion of the small-scale bright ring features in the optical, X-ray, and radio do not represent the expansion of the reverse shock, but rather represent a brightness-weighted average of ejecta passing through and being decelerated by the reverse shock. The motion of the reverse shock itself is then represented by the motion of the angle-averaged emissivity profile of the radio bright ring.
Warming and Ocean Acidification Effects on Phytoplankton—From Species Shifts to Size Shifts within Species in a Mesocosm Experiment

While the isolated responses of marine phytoplankton to climate warming and to ocean acidification have been studied intensively, studies on the combined effect of both aspects of Global Change are still scarce. Therefore, we performed a mesocosm experiment with a factorial combination of temperature (9 and 15°C) and pCO2 (means: 439 ppm and 1040 ppm) with a natural autumn plankton community from the western Baltic Sea. Temporal trajectories of total biomass and of the biomass of the most important higher taxa followed similar patterns in all treatments. When averaging over the entire time course, phytoplankton biomass decreased with warming and increased with CO2 under warm conditions. The contribution of the two dominant higher phytoplankton taxa (diatoms and cryptophytes) and of the 4 most important species (3 diatoms, 1 cryptophyte) did not respond to the experimental treatments. Taxonomic composition of phytoplankton showed only responses at the level of subdominant and rare species. Phytoplankton cell sizes increased with CO2 addition and decreased with warming. Both effects were stronger for larger species. Warming effects were stronger than CO2 effects and tended to counteract each other. Phytoplankton communities without calcifying species and exposed to short-term variation of CO2 seem to be rather resistant to ocean acidification.
Group Factor Analysis

Factor analysis (FA) provides linear factors that describe the relationships between individual variables of a data set. We extend this classical formulation into linear factors that describe the relationships between groups of variables, where each group represents either a set of related variables or a data set. The model also naturally extends canonical correlation analysis to more than two sets, in a way that is more flexible than previous extensions. Our solution is formulated as a variational inference of a latent variable model with structural sparsity, and it consists of two hierarchical levels: 1) the higher level models the relationships between the groups and 2) the lower models the observed variables given the higher level. We show that the resulting solution solves the group factor analysis (GFA) problem accurately, outperforming alternative FA-based solutions as well as more straightforward implementations of GFA. The method is demonstrated on two life science data sets, one on brain activation and the other on systems biology, illustrating its applicability to the analysis of different types of high-dimensional data sources.
Plant and Bird Presence Strongly Influences the Microbial Communities in Soils of Admiralty Bay, Maritime Antarctica

Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
Cosmological H II Bubble Growth during Reionization

We present general properties of ionized hydrogen (H II) bubbles and their growth based on a state-of-the-art, large-scale (100 Mpc h−1) cosmological radiative transfer simulation. The simulation resolves all halos with atomic cooling at the relevant redshifts and simultaneously performs radiative transfer and dynamical evolution of structure formation. Our major conclusions include the following: (1) For significant H II bubbles, the number distribution is peaked at a volume of ~0.6 Mpc3 h−3 at all redshifts. But at z ⩽ 10, one large, connected network of bubbles dominates the entire H II volume. (2) H II bubbles are highly nonspherical. (3) The H II regions are highly biased with respect to the underlying matter distribution, with the bias decreasing with time. (4) The non-Gaussianity of the H II region is small when the universe becomes 50% ionized. The non-Gaussianity reaches its maximum near the end of the reionization epoch z ∼ 6. But at all redshifts of interest there is a significant non-Gaussianity in the H II field. (5) Population III galaxies may play a significant role in the reionization process. Small bubbles are initially largely produced by Population III stars. At z ⩾ 10 even the largest H II bubbles have a balanced ionizing photon contribution from Population II and Population III stars, while at z ⩽ 8 Population II stars start to dominate the overall ionizing photon production for large bubbles, although Population III stars continue to make a nonnegligible contribution. (6) The relationship between halo number density and bubble size is complicated, but a strong correlation is found between halo number density and bubble size for large bubbles.
The influence of patient's consciousness regarding high blood pressure and patient's attitude in face of disease controlling medicine intake.

OBJECTIVE To assess the relation between blood pressure control and the following: the Morisky-Green test, the patient's consciousness regarding high blood pressure, the patient's attitude in face of medicine intake, the patient's attendance at medical consultations, and the subjective physician's judgment. METHODS We studied 130 hypertensive patients with the following characteristics: 73% females, 60 +/- 11 years, 58% married, 70% white, 45% retired, 45% with incomplete elementary schooling, 64% had a familial income of 1 to 3 minimum wages, body mass index of 30 +/- 7 kg/m , consciousness regarding the disease for a mean period of 11 +/- 9.5 years, and mean treatment duration of 8 +/- 7 years. RESULTS Only 35% of the hypertensive individuals had blood pressure under control and a longer duration of treatment (10 +/- 7 vs 7 +/- 6.5 years; P<0.05). The retiree predominated. The result of the Morisky-Green test did not relate to blood pressure control. In evaluating the attitude in face of medicine intake, the controlled patients achieved significantly higher scores than did the noncontrolled patients (8 +/- 1.9 vs 7 +/- 2, P<0.05). The hypertensive patients had higher levels of consciousness regarding their disease and its treatment, and most (70%) patients attended 3 or 4 medical consultations, which did not influence blood pressure control. The physicians attributed significantly higher scores regarding adherence to treatment to controlled patients (6 +/- 0.8 vs 5 +/- 1.2; P<0.05). CONCLUSION Consciousness regarding the disease, the Morisky-Green test, and attendance to medical consultations did not influence blood pressure control.
Key Concepts

When scholars problematize is/ought inferences (IOI's), they sometimes refer to Hume's or Moore's fallacy (e. Although inferring " ought " from " is " can be problematic, we argue that, in the context of contemporary IOI's in the cognitive sciences, invoking Hume or Moore might be misguided. This is because Hume's and Moore's arguments concern the validity and soundness of deductive inferences while in our view contemporary IOI's in the cognitive sciences are better interpreted as defeasible inferences. In order to avoid misinterpretations, we first clarify key concepts in the debate in section Key Concepts. In section Mind the Gap, we revisit Hume's and Moore's arguments against inferring " ought " from " is, " and in section A Debate Shackled, we discuss contemporary IOI's in the cognitive sciences. Participants in the is/ought debate distinguish between descriptive statements and deontic statements. Descriptive statements describe or predict how the world is. Deontic statements prescribe or proscribe how we should act or reason. While " is " statements are descriptive statements, " ought " statements can be descriptive as well as deontic. For instance, " the streets ought to be wet because it is raining " is a descriptive statement because it predicts that the streets will be wet. Conversely, " If you do not want to get wet, you ought to carry an umbrella, " is a deontic statement because it prescribes what you should do. In this comment, we only discuss " ought " statements as deon-tic statements. Accordingly, we will not discuss inferences from " is " to descriptive " oughts " (cf. Oaksford and Chater, 2009, 2011), but only inferences from " is " to deontic " oughts " (cf. Oaksford and Sellen, 2000; Stanovich and West, 2000). We describe an is/ought inference as an attempt to evaluate (i.e., fine-tune, develop, arbitrate between) deontic statements on the basis of descriptive statements. The following is an example of an IOI: (1) Premise: More intelligent people are more likely than less intelligent people to make a guess, instead of reason , when solving the Wason Selection Task. Conclusion: We ought to make a guess, instead of reason, when solving the Wason Selection Task. This inference can be interpreted as a deductive argument. As such, the conclusion is true if the inference is valid and sound. A deductive inference is valid if the premises logically entail the conclusions , hence, if …
Local anesthesia for pain control during transrectal ultrasound-guided prostate biopsy: a systematic review and meta-analysis

Background A meta-analysis was performed to evaluate the efficacy and safety of intrarectal local anesthestic (IRLA), periprostatic nerve block (PPNB), and the combined modalities in alleviating the pain during transrectal ultrasound (TRUS)-guided prostate biopsy. Materials and methods A literature review was performed to identify all published randomized controlled trials (RCTs) about IRLA vs no anesthesia or placebo gel; PPNB vs no injection, periprostatic placebo injection, or IRLA; combined PPNB and IRLA vs PPNB alone; and combined PPNB and intraprostatic nerve block (IPNB) vs PPNB alone before TRUS-guided biopsy. Sources included MEDILINE, EMBASE, and Cochrane Library from 1980 to 2016. The main outcomes were biopsy pain score, probe manipulation pain score, and anesthetic infiltration pain score assessed by the visual pain scale. Results A total of 26 articles involving 36 RCTs were used in this analysis: Although IRLA can lead to pain reduction, the result was not statistically significant when compared with no anesthesia or placebo gel (weighted mean difference [WMD]: −0.22, 95% CI: −0.45 to 0, P=0.06). PPNB can lead to significantly lower biopsy pain scores when compared with no analgesia (WMD: −1.32, 95% CI: −1.68 to −0.95, P<0.00001), placebo injection (WMD: −2.62, 95% CI: −3.16 to −2.07, P<0.00001), or IRLA (WMD: −1.31, 95% CI: −1.40 to −1.22, P<0.00001). PPNB + IRLA can lead to significantly lower biopsy pain scores when compared with PPNB alone (WMD: −0.45, 95% CI: −0.62 to −0.28, P<0.00001). PPNB + IPNB can lead to significantly lower biopsy pain scores when compared with PPNB alone (WMD: −0.73, 95% CI: −0.92 to −0.55, P<0.00001). There were no severe reported general or local complications related to local anesthesia. Conclusion This meta-analysis indicates that a combination of PPNB and IRLA/IPNB is effective and safe in alleviating the pain during TRUS-guided prostate biopsy. Further high-quality RCTs are needed to validate this result.
Cost recurrences for DML programs

A cost recurrence describes an upper bound for the running time of a program in terms of the size of its input. Finding cost recurrences is a frequent intermediate step in complexity analysis, and this step requires an abstraction from data to data size. In this article, we use information contained in dependent types to achieve such an abstraction: Dependent ML (DML), a conservative extension of ML, provides dependent types that can be used to associate data with size information, thus describing a possible abstraction. We automatically extract cost recurrences from first-order DML programs, guiding the abstraction from data to data size with information contained in DML type derivations.
Rapid genotyping of melanocortin-1 receptor with use of fluorescence-labeled oligonucleotides.

The melanocortin-1 receptor (MC1R), localized on chromosome 16q24.3, is a G-protein-coupled receptor expressed mostly in melanocytes. Melanotropic ligands such as α-melanocyte-stimulating hormone and adrenocorticotropic hormone act via MC1R and regulate the proportion of the photo-protective melanins eumelanin and pheomelanin, which may contribute to ultraviolet (UV) radiation-induced skin damage (1) by favoring the synthesis of eumelanin. Individuals with red hair have a predominance of pheomelanin in hair and skin and/or a reduced ability to produce eumelanin, which may explain why they fail to tan and suffer from increased cutaneous UV sensitivity and why UV irradiation is more dangerous for them. Fair skin and red hair are also associated with an increased risk of cutaneous malignant melanoma (2)(3). Recently, some polymorphic variants of MC1R have been associated with red hair and found to be overrepresented in individuals with fair skin (4)(5)(6)(7), particularly the Arg151Cys, Arg160Trp, and Asp294His variants (1)(4 …
The effects of exercise and stress on the survival and maturation of adult‐generated granule cells

Stress strongly inhibits proliferation of granule cell precursors in the adult dentate gyrus, whereas voluntary running has the opposite effect. Few studies, however, have examined the possible effects of these environmental manipulations on the maturation and survival of young granule cells. We examined the number of surviving granule cells and the proportion of young neurons that were functionally mature, as defined by seizure‐induced immediate‐early gene (IEG) expression, in 14‐ and 21‐day‐old granule cells in mice that were given access to a running wheel, restrained daily for 2 h, or given no treatment during this period. Treatments began 2 days after BrdU injection, to isolate effects on survival from those on cell proliferation. We found a large increase in granule cell survival in running mice when compared with controls at both time points. In addition, running increased the proportion of granule cells expressing the IEG Arc in response to seizures, suggesting that it speeds incorporation into circuits, i.e., functional maturation. Stressed mice showed no change in Arc expression, compared with control animals, but, surprisingly, showed a transient increase in survival of 14‐day‐old granule cells, which was gone 7 days later. Examination of cell proliferation, using the endogenous mitotic marker PCNA showed an increase in cell proliferation after 12 days of running but not after 19 days of running. The number of proliferating cells was unchanged 24 h after the 12th or 19th episode of daily restraint stress. These findings demonstrate that running has strong effects on survival and maturation of young granule cells as well as their birth and that stress can have positive but short‐lived effects on granule cell survival. Published 2009 Wiley‐Liss, Inc.
Regional astrocyte IFN signaling restricts pathogenesis during neurotropic viral infection

Type I IFNs promote cellular responses to viruses, and IFN receptor (IFNAR) signaling regulates the responses of endothelial cells of the blood-brain barrier (BBB) during neurotropic viral infection. However, the role of astrocytes in innate immune responses of the BBB during viral infection of the CNS remains to be fully elucidated. Here, we have demonstrated that type I IFNAR signaling in astrocytes regulates BBB permeability and protects the cerebellum from infection and immunopathology. Mice with astrocyte-specific loss of IFNAR signaling showed decreased survival after West Nile virus infection. Accelerated mortality was not due to expanded viral tropism or increased replication. Rather, viral entry increased specifically in the hindbrain of IFNAR-deficient mice, suggesting that IFNAR signaling critically regulates BBB permeability in this brain region. Pattern recognition receptors and IFN-stimulated genes had higher basal and IFN-induced expression in human and mouse cerebellar astrocytes than did cerebral cortical astrocytes, suggesting that IFNAR signaling has brain region–specific roles in CNS immune responses. Taken together, our data identify cerebellar astrocytes as key responders to viral infection and highlight the existence of distinct innate immune programs in astrocytes from evolutionarily disparate regions of the CNS.