Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffeomorphic Point Matching with Applications in Biomedical Image Registration

The need for 3D diffeomorphic matching of unlabeled point sets arises in numerous registration and shape analysis oriented biomedical imaging applications. The correspondence problem coupled with the need for estimating a diffeomorphism in 3D space makes it a very difficult problem. In the present work, we show that a joint clustering and diffeomorphism estimation strategy is capable of simultaneously estimating correspondences and a diffeomorphism in 3D space to interpolate the two unlabeled point sets. Correspondence is established between the cluster centers. Cluster centers for the two point sets having the same labels are always in correspondence. Essentially, as the cluster centers evolve during the iterations of an incremental EM algorithm, we estimate a diffeomorphism in 3D space. The approach is completely symmetric w.r. t. inversion of the two point sets being matched. We demonstrate our approach on 3D hippocampal data.
Hybridization in Situ Fluorescence Locus in B-Cell Chronic Lymphocytic Leukemia Revealed by D 13 S 25 and the RB1 Heterogeneity of Deletions Involving Updated

Recently, the D13S25 locus, which is in close proximity to the retinoblastoma gene (RB-1 ) on chromosome band 13ql4, was discussed to play a role in the pathogenesis of B-CLL. In the present study, we isolated two overlapping genomic DNA clones (termed cl3S25) containing the DI3S25 DNA segment and used them as probes to analyze 85 B-CLL cases by fluorescence in situ hybridization; of the 55 cases with two RB-1 copies, 13 exhibited hemizygous (n = 7) or homozygous (n = 6) deletion OÃ•D13S25. Of 29 cases with hemizygous deletion ot'KH-l, all but two also showed loss of D13S25 (hemizygous, n = 25; homozygous, n = 2). One case had a homozygous deletion of both loci. We conclude that deletion of DI3S25 occurs in a substantial number of B-CLL without deletion of Hli-l. However, in some cases there is deletion of RB-1 without loss of D13S25, suggesting that D13S25 is not the locus of the putative tumor suppressor gene. According to our data, such a gene is most likely located within the genomic region between D13S25 and RB-1.
Primate frontal eye fields. I. Single neurons discharging before saccades.

We studied the activity of single neurons in the frontal eye fields of awake macaque monkeys trained to perform several oculomotor tasks. Fifty-four percent of neurons discharged before visually guided saccades. Three different types of presaccadic activity were observed: visual, movement, and anticipatory. Visual activity occurred in response to visual stimuli whether or not the monkey made saccades. Movement activity preceded purposive saccades, even those made without visual targets. Anticipatory activity preceded even the cue to make a saccade if the monkey could reliably predict what saccade he had to make. These three different activities were found in different presaccadic cells in different proportions. Forty percent of presaccadic cells had visual activity (visual cells) but no movement activity. For about half of the visual cells the response was enhanced if the monkey made saccades to the receptive-field stimulus, but there was no discharge before similar saccades made without visual targets. Twenty percent of presaccadic neurons discharged as briskly before purposive saccades made without a visual target as they did before visually guided saccades, and had weak or absent visual responses. These cells were defined as movement cells. Movement cells discharged much less or not at all before saccades made spontaneously without a task requirement or an overt visual target. The remaining presaccadic neurons (40%) had both visual and movement activity (visuomovement cells). They discharged most briskly before visually guided eye movements, but also discharged before purposive eye movements made in darkness and responded to visual stimuli in the absence of saccades. There was a continuum of visuomovement cells, from cells in which visual activity predominated to cells in which movement activity predominated. This continuum suggests that although visual cells are quite distinct from movement cells, the division of cell types into three classes may be only a heuristic means of describing the processing flow from visual input to eye-movement output. Twenty percent of visuomovement and movement cells, but fewer than 2% of visual cells, had anticipatory activity. Only one cell had anticipatory activity as its sole response. When the saccade was delayed relative to the target onset, visual cells responded to the target appearance, movement cells discharged before the saccade, and visuomovement cells discharged in different ways during the delay, usually with some discharge following the target and an increase in rate immediately before the saccade. Presaccadic neurons of all types were actively suppressed following a saccade into their response fields. (ABSTRACT TRUNCATED AT 400 WORDS)
14 HISTAMINE

In a certain way, histaminergic systems have had a great, although indirect, historical importance in the development of neuropsychopharmacology. Indeed, the discovery of both the neuroleptic agents and the tricyclic antidepressant drugs in the 1950s was derived from the clinical study of behavioral actions of ‘‘antihistamines,’’ a class of antiallergic drugs now designated H1-receptor antagonists. Nevertheless, the histaminergic neuronal system in the brain, although already understood by the mid-1970s, has remained largely unexploited in drug design. Thus, only the traditional brain-penetrating H1-receptor antagonists, used as over-the-counter sleeping pills, are known to interfere with histaminergic transmissions in the central nervous system (CNS). This situation contrasts with the emergence, in the 1990s, of detailed knowledge of the system that revealed that it shares many biological and functional properties with other aminergic systems overexploited in CNS drug design. Histamine and its receptors in the brain have been the subject of two comprehensive reviews (1,2). Therefore, to limit the length of the present chapter, we have deliberately elected to summarize the detailed information that can be found in these reviews and have added only more recent information and major references.
Methanogens at the top of the world: occurrence and potential activity of methanogens in newly deglaciated soils in high-altitude cold deserts in the Western Himalayas

Methanogens typically occur in reduced anoxic environments. However, in recent studies it has been shown that many aerated upland soils, including desert soils also host active methanogens. Here we show that soil samples from high-altitude cold deserts in the western Himalayas (Ladakh, India) produce CH4 after incubation as slurry under anoxic conditions at rates comparable to those of hot desert soils. Samples of matured soil from three different vegetation belts (arid, steppe, and subnival) were compared with younger soils originating from frontal and lateral moraines of receding glaciers. While methanogenic rates were higher in the samples from matured soils, CH4 was also produced in the samples from the recently deglaciated moraines. In both young and matured soils, those covered by a biological soil crust (biocrust) were more active than their bare counterparts. Isotopic analysis showed that in both cases CH4 was initially produced from H2/CO2 but later mostly from acetate. Analysis of the archaeal community in the in situ soil samples revealed a clear dominance of sequences related to Thaumarchaeota, while the methanogenic community comprised only a minor fraction of the archaeal community. Similar to other aerated soils, the methanogenic community was comprised almost solely of the genera Methanosarcina and Methanocella, and possibly also Methanobacterium in some cases. Nevertheless, ~103 gdw−1 soil methanogens were already present in the young moraine soil together with cyanobacteria. Our results demonstrate that Methanosarcina and Methanocella not only tolerate atmospheric oxygen but are also able to survive in these harsh cold environments. Their occurrence in newly deglaciated soils shows that they are early colonizers of desert soils, similar to cyanobacteria, and may play a role in the development of desert biocrusts.
Functional topography of cat primary auditory cortex: distribution of integrated excitation.

1. Neuronal responses to tones and transient stimuli were mapped with microelectrodes in the primary auditory cortex (AI) of barbiturate anesthetized cats. Most of the dorsoventral extent of AI was mapped with multiple-unit recordings in the high-frequency domain (between 5.8 and 26.3 kHz) of all six studied cases. The spatial distributions of 1) sharpness of tuning measured with pure tones and 2) response magnitudes to a broadband transient were determined in each of three intensively studied cases. 2. The sharpness of tuning of integrated cluster responses was defined 10 dB above threshold (Q10 dB, integrated excitatory bandwidth). The spatial reconstructions revealed a frequency-independent maximum located near the center of the dorsoventral extent of AI. The sharpness of tuning gradually decreased toward the dorsal and ventral border of AI in all three cases. 3. The sharpness of tuning 40 dB above response threshold was also analyzed (Q40 dB). The Q40 dB values were less than one-half of the corresponding Q10 dB value. The spatial distribution showed a maximum in the center of AI, similar to the Q10 dB distribution. In two out of three cases, restricted additional maxima were recorded dorsal to the main maximum. Overall, Q10 dB and Q40 dB were only moderately correlated, indicating that the integrated excitatory bandwidth at higher stimulus levels can be influenced by additional mechanisms that are not active at lower levels. 4. The magnitude of excitatory responses to a broadband transient (frequency-step response) was determined. The normalized response magnitude varied between less than 1% and up to 100% relative to a characteristic frequency (CF) tone response. The step-response magnitude showed a systematic spatial distribution. An area dorsal to the Q10 dB maximum consistently showed the largest response magnitude surrounded by areas of lower responsivity. A second spatially more restricted maximum was recorded in the ventral-third of each map. Areas with high-transient responsiveness coincided with areas of broad integrated excitatory bandwidth at comparable stimulus levels. 5. The distribution of excitation produced by narrowband and broadband signals suggest that there exists a clear functional organization in the isofrequency domain of AI that is orthogonal to the main cochleotopic organization of the AI. Systematic spatial variations of the integrated excitatory bandwidth reflect underlying cortical processing capacities that may contribute to a parallel analysis of spectral complexity, e.g., spectral shape and contrast, at any given frequency. (ABSTRACT TRUNCATED AT 400 WORDS)
Toward a full test of the $\nu$MSM sterile neutrino dark matter model with Athena

We discuss the potential of Athena X-ray telescope, in particular of its X-ray Integral Field Unit (X-IFU), for detection of the signal from the light-weight decaying dark matter with mass in the keV range. We show that high energy resolution and large collection area of X-IFU will provide an improvement of sensitivity which will be sufficient for the full test of the neutrino Minimal extension of the Standard Model (nuMSM). Search for the narrow spectral line produced by the decay of the dark matter sterile neutrino in the spectra of dwarf spheroidal galaxies with X-IFU will explore the whole allowed range masses and mixing angles of the nuMSM lightest sterile neutrino and in this way either to find the dark matter signal or rule out the nuMSM model.
IL-4-Induced GATA-3 Expression Is a Time-Restricted Instruction Switch for Th2 Cell Differentiation1

An initial activation signal via the TCR in a restricted cytokine environment is critical for the onset of Th cell development. Cytokines regulate the expression of key transcriptional factors, T-bet and GATA-3, which instruct the direction of Th1 and Th2 differentiation, through changes in chromatin conformation. In this study, we investigated the kinetics of IL-4-mediated signaling in a transgenic mouse, expressing human IL-4R on a mouse IL-4αR-deficient background. These experiments, allowing induction with human IL-4 at defined times, demonstrated that an IL-4 signal was required at the early stage of TCR-mediated T cell activation for lineage commitment to Th2, along with structural changes in chromatin, which take place in the conserved noncoding sequence-1 and -2 within the IL-4 locus. At later times, however, IL-4 failed to promote efficient Th2 differentiation and decondensation of chromatin, even though GATA-3 was clearly induced in the nuclei by IL-4 stimulation. Moreover, IL-4-mediated Th2 instruction was independent from cell division mediated by initial TCR stimulation. The role of IL-4 signaling may have a time restriction during Th2 differentiation. In late stages of initial T cell activation, the chromatin structure of the IL-4 locus retains condensation state. These results demonstrate that IL-4-induced GATA-3 expression is time-restriction switch for Th2 differentiation.
An assessment of the temporal dynamics of moral decisions

In the domain of moral decision making, models in which emotion and deliberation constitute competing dual-systems have become increasingly popular. Currently, the favored explanation of this interaction is what Evans (2008) termed a “default-interventionist” (DI) process where moral decisions are the result of a prepotent emotional response, which can be overridden with substantial deliberative effort. Although this “emotion-then-deliberation” sequence is often assumed, existing methods have lacked the requisite process resolution to clearly depict the nature of this interaction. The present work utilized continuous mouse tracking, or response dynamics, to develop and test predictions of these DI models of moral decision making. Study 1 utilized previously published moral dilemmas to validate the method for use with such complex stimuli. Although the data replicated typical choice and RT patterns, the process metrics provided by the response trajectories did not demonstrate the online preference reversals predicted by DI models. Study 2 utilized more rigorously constructed stimuli and an alternative presentation format to provide the strongest possible test of DI predictions, but again failed to show the predicted reversals. In summary, neither experiment provided data in accordance with the predictions of popular DI dual-systems models, which suggests that researchers should consider models allowing for concurrent activation of deliberative and emotional systems, or reconceptualize moral decisions within the typical multiattribute decision framework.
A Reexamination of the PPAR-α Activation Mode of Action as a Basis for Assessing Human Cancer Risks of Environmental Contaminants

Background Diverse environmental contaminants, including the plasticizer di(2-ethylhexyl)phthalate (DEHP), are hepatocarcinogenic peroxisome proliferators in rodents. Peroxisome proliferator–activated receptor-α (PPAR-α) activation and its sequelae have been proposed to constitute a mode of action (MOA) for hepatocarcinogenesis by such agents as a sole causative factor. Further, based on a hypothesized lower sensitivity of humans to this MOA, prior reviews have concluded that rodent hepatocarcinogenesis by PPAR-α agonists is irrelevant to human carcinogenic risk. Data synthesis Herein, we review recent studies that experimentally challenge the PPAR-α activation MOA hypothesis, providing evidence that DEHP is hepatocarcinogenic in PPAR-α–null mice and that the MOA but not hepatocarcinogenesis is evoked by PPAR-α activation in a transgenic mouse model. We further examine whether relative potency for PPAR-α activation or other steps in the MOA correlates with tumorigenic potency. In addition, for most PPAR-α agonists of environmental concern, available data are insufficient to characterize relative human sensitivity to this rodent MOA or to induction of hepatocarcinogenesis. Conclusions Our review and analyses raise questions about the hypothesized PPAR-α activation MOA as a sole explanation for rodent hepatocarcinogenesis by PPAR-α agonists and therefore its utility as a primary basis for assessing human carcinogenic risk from the diverse compounds that activate PPAR-α. These findings have broad implications for how MOA hypotheses are developed, tested, and applied in human health risk assessment. We discuss alternatives to the current approaches to these key aspects of mechanistic data evaluation.
Effect of the Survival Judgment Task on Memory Performance in Subclinically Depressed People

Many reports have described that a survival judgment task that requires participants to judge words according to their relevance to a survival situation can engender better recall than that obtained in other judgment tasks such as semantic or self-judgment tasks. We investigated whether memory enhancement related to the survival judgment task is elicited or not in subclinically depressed participants. Based on the BDI score, participants were classified as either depressed or non-depressed participants. Then 20 depressed participants and 24 non-depressed participants performed a survival judgment task and an autobiographical recall task. Results showed memory enhancement related to the survival judgment task in both depressed and non-depressed participants, but showed lower memory enhancement related to the survival judgment task in depressed participants than in non-depressed participants. These results suggest that the survival judgment task benefit is a robust phenomenon. Moreover, that benefit was reduced by depressed emotion. The combination hypothesis better explains the mechanism of memory enhancement related to the survival judgment task than the functional, emotional, and arousal or congruency hypothesis does.
On the temporal evolution of backbone topological robustness

As society progressively depends on large-scale telecommunications networks and their connectivity rapidly rises over time, it becomes of vital importance to study their topological features. On the backbone level uncertain disturbances of its constituent parts may affect a sizable proportion of the population, thus this can well explain the recent focus on evaluating backbone robustness metrics. Unlike previous empirical studies, which are limited to static snapshots of topologies, in this paper robustness algorithms are applied to networks over time. The temporal evolution of topological robustness is studied for a set of four real backbone networks by observing snapshots taken at regularly spaced points in time. It is found that only half of the fundamental robustness properties are changing over time with even fewer improving their values. The introduction of the time factor extends the robustness analysis and allows for deriving results on the network robustness dynamics.
The Human Capital Cost of Landmine Contamination in Cambodia

The International Campaign to Ban Landmines production and use estimates that there are more than 80 billion landmines in the ground in more than 80 countries. Despite the scale of the problem and large investments by OECD countries to clear mines in low income countries, the economic consequences of landmine contamination have been so far unexamined by economists working on the economics of wars, perhaps due to the lack of data thus far. Using unique data from Cambodia, this paper estimates the effect of landmine contamination on human capital. These effects are identified using difference-in-differences (DD) and instrumental variables (IV) estimators. In the DD framework I exploit two sources of variation in an individual’s exposure to the conflict: her age in 1970 due to the spread of landmines over time and landmine contamination intensity in her district of birth. The IV specification uses the distance to the Thai border as an exogenous source of variation in landmine contamination intensity. The IV estimate indicates a education loss of 0.4 years at the mean and no visible effect on earnings. I discuss three factors that probably drive down the returns to education in post-war Cambodia: (1) The downgrading of educated people during the Khmer rouge regime (2) Direct Effects of landmines on the returns to education (3) the destruction of physical capital and technological delay through capital-skill complementarity.
Self-Compassion, Emotion Regulation and Stress among Australian Psychologists: Testing an Emotion Regulation Model of Self-Compassion Using Structural Equation Modeling

Psychologists tend to report high levels of occupational stress, with serious implications for themselves, their clients, and the discipline as a whole. Recent research suggests that self-compassion is a promising construct for psychologists in terms of its ability to promote psychological wellbeing and resilience to stress; however, the potential benefits of self-compassion are yet to be thoroughly explored amongst this occupational group. Additionally, while a growing body of research supports self-compassion as a key predictor of psychopathology, understanding of the processes by which self-compassion exerts effects on mental health outcomes is limited. Structural equation modelling (SEM) was used to test an emotion regulation model of self-compassion and stress among psychologists, including postgraduate trainees undertaking clinical work (n = 198). Self-compassion significantly negatively predicted emotion regulation difficulties and stress symptoms. Support was also found for our preliminary explanatory model of self-compassion, which demonstrates the mediating role of emotion regulation difficulties in the self-compassion-stress relationship. The final self-compassion model accounted for 26.2% of variance in stress symptoms. Implications of the findings and limitations of the study are discussed.
Biochemical Markers of Myocardial Damage

Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in clinical practice.