Miracle-dz/UniFAR-FTUs huggingface dataset:
Cardiac injury after chest trauma

Fifty consecutive patients with severe chest trauma were studied prospectively to evaluate the frequency of significant cardiac injury and to determine what diagnostic studies were useful. Forty-nine of 50 patients had elevated cardiac enzymes and 26 of 50 had abnormal ECGs on admission. No patient had complications associated with myocardial infarction, including 15 who underwent general anesthesia. We found persistent (greater than 48 h) ECG changes in only 3, 2 of these 3 also had markedly elevated MB fraction of CPK. Significant pericarditis occurred in 5 patients, 2 of whom never had ECG abnormalities.We conclude that minor cardiac injury is common in severe chest trauma, but only rarely causes myocardial contusion. Myocardial isoenzymes may be useful in making that important distinction. Clinically significant traumatic pericarditis may occur in the absence of ECG changes and must be considered in every patient with chest injury and unstable hemodynamics.
MPE and Partial Inversion in Lifted Probabilistic Variable Elimination

It is often convenient to represent probabilistic models in a first-order fashion, using logical atoms such as partners (X, Y) as random variables parameterized by logical variables. (de Salvo Braz, Amir, & Roth 2005), following (Poole 2003), give a lifted variable elimination algorithm (FOVE) for computing marginal probabilities from first-order probabilistic models (belief assessment, or BA). FOVE is lifted because it works directly at the first-order level, eliminating all the instantiations of a set of atoms in a single step, in some cases independently of the number of these instantiations. Previous work could treat only restricted potential functions. There, atoms' instantiations cannot constrain each other: predicates can appear at most once, or logical variables must not interact across atoms. In this paper, we present two contributions. The first one is a significantly more general lifted variable elimination algorithm, FOVE-P, that covers many cases where atoms share logical variables. The second contribution is to use FOVE-P for solving the Most Probable Explanation (MPE) problem, which consists of calculating the most probable assignment of the random variables in a model. The transition from BA to MPE is straightforward in propositional models, but the lifted first-order case is harder. We introduce the notion of lifted assignments, a distribution of values to a set of random variables rather than to each individual one. Lifted assignments are cheaper to compute while being as useful as regular assignments over that group. Both contributions advance the theoretical understanding of lifted probabilistic inference.
Phosphorylation of the Transcription Factor YY1 by CK2α Prevents Cleavage by Caspase 7 during Apoptosis

ABSTRACT In this report, we describe the phosphorylation of Yin Yang 1 (YY1) in vitro and in vivo by CK2α (casein kinase II), a multifunctional serine/threonine protein kinase. YY1 is a ubiquitously expressed multifunctional zinc finger transcription factor implicated in regulation of many cellular and viral genes. The products of these genes are associated with cell growth, the cell cycle, development, and differentiation. Numerous studies have linked YY1 to tumorigenesis and apoptosis. YY1 is a target for cleavage by caspases in vitro and in vivo as well, but very little is known about the mechanisms that regulate its cleavage during apoptosis. Here, we identify serine 118 in the transactivation domain of YY1 as the site of CK2α phosphorylation, proximal to a caspase 7 cleavage site. CK2α inhibitors, as well as knockdown of CK2α by small interfering RNA, reduce S118 phosphorylation in vivo and enhance YY1 cleavage under apoptotic conditions, whereas increased CK2α activity by overexpression in vivo elevates S118 phosphorylation. A serine-to-alanine substitution at serine 118 also increases the cleavage of YY1 during apoptosis compared to wild-type YY1. Taken together, we have discovered a regulatory link between YY1 phosphorylation at serine 118 and regulation of its cleavage during programmed cell death.
ISOTONIC SALINE DIURESIS AND URINARY CONCENTRATING ABILITY IN RENAL HYPERTENSIVE RATS.

In rats made hypertensive by constricting one renal artery, the ‘clamped’ kidney could not elaborate a maximally concentrated urine after dehydration and under the influence of exogenous vasopressin. The diuretic response to the intravenous infusion of 0.86 ± 0.04 ml/kg min of 0.15 M NaCl solution was smaller in the ‘clamped’ than in a normal kidney: the urinary sodium and potassium concentrations were very low. The functional changes observed were already present a few hours after ‘clamping’ and, thus, preceded the development of hypertension and changes in renal renin concentration. In the ‘undamped’ kidney of the renal hypertensive rat salt and water were excreted 25 to 30% more rapidly than in a normal kidney at high rates of intravenous saline infusion. In intact renal hypertensive rats receiving intravenous saline at different rates, GFR (CIn) and salt water excretion rates were the same as in normal controls. The enhanced diuretic response to oral saline loads must, therefore, be ascribed mainly to extrarenal changes.
Detection of herpes simplex virus in conventional tube cell cultures and in shell vials with a DNA probe kit and monoclonal antibodies

Specimens submitted for diagnosis of herpes simplex virus (HSV) infection were inoculated into shell vials and reacted with a commercial DNA probe kit (Pathogene; Enzo Biochem, Inc., New York, N.Y.) and an immunofluorescence assay at 16 h postinoculation. The results were compared with isolation of the virus in conventional tube cell cultures. Of 504 specimens, 105 (20.8%) were positive for HSV. Of the 105, 93 HSV-positive specimens (89%) were detected by all three assay systems. Maximum detection of HSV (100 of 105 [95%]) was obtained by probe or monoclonal antibody assay in shell vials, which had sensitivities of 98 and 97%, respectively, compared with viral recovery in conventional tube cell cultures (mean time for recognition of cytopathic effects, 2 days). Both shell vial assays were 99% specific. The DNA probe kit may be used as an alternative to a monoclonal antibody and fluorescence assay in shell vials as a diagnostic method for rapid laboratory detection of HSV infection.
Microbial Ecology of Arsenic Contaminated Aquifers and Potential Bioremediation

Subsurface removal of arsenic by injection with oxygenated groundwater has been proposed as a viable technology for obtaining “safe” drinking water in Bangladesh. While the oxidation of ferrous iron to solid ferric iron minerals, to which arsenic adsorbs, is assumed to be driven by abiotic reactions, metal-cycling microorganisms may potentially affect arsenic removal. A cultivation-independent survey covering 24 drinking water wells in several geographical regions in Bangladesh was conducted to obtain information on microbial community structure and diversity in general, and on specific functional groups capable of the oxidation or reduction of arsenic or iron. Each functional group, targeted by either groupspecific 16S rRNA or functional gene amplification, occurred in at least 79% of investigated samples. Putative arsenate reducers and iron-oxidizing Gallionellaceae were present at low diversity, while more variation in potentially arsenite-oxidizing microorganisms and ironreducing Desulfuromonadales was revealed within and between samples. Relations between community composition on the one hand and hydrochemistry on the other hand were in general not evident, apart from an impact of salinity on iron-cycling microorganisms. Our data suggest widespread potential for a positive contribution of arsenite and iron oxidizers to arsenic removal upon injection with oxygenated water, but also indicate a potential risk for arsenic re-mobilization by anaerobic arsenate and iron reducers once injection is halted.
A Fully Integrated Wireless Compressed Sensing Neural Signal Acquisition System for Chronic Recording and Brain Machine Interface

Reliable, multi-channel neural recording is critical to the neuroscience research and clinical treatment. However, most hardware development of fully integrated, multi-channel wireless neural recorders to-date, is still in the proof-of-concept stage. To be ready for practical use, the trade-offs between performance, power consumption, device size, robustness, and compatibility need to be carefully taken into account. This paper presents an optimized wireless compressed sensing neural signal recording system. The system takes advantages of both custom integrated circuits and universal compatible wireless solutions. The proposed system includes an implantable wireless system-on-chip (SoC) and an external wireless relay. The SoC integrates 16-channel low-noise neural amplifiers, programmable filters and gain stages, a SAR ADC, a real-time compressed sensing module, and a near field wireless power and data transmission link. The external relay integrates a 32 bit low-power microcontroller with Bluetooth 4.0 wireless module, a programming interface, and an inductive charging unit. The SoC achieves high signal recording quality with minimized power consumption, while reducing the risk of infection from through-skin connectors. The external relay maximizes the compatibility and programmability. The proposed compressed sensing module is highly configurable, featuring a SNDR of 9.78 dB with a compression ratio of 8×. The SoC has been fabricated in a 180 nm standard CMOS technology, occupying 2.1 mm × 0.6 mm silicon area. A pre-implantable system has been assembled to demonstrate the proposed paradigm. The developed system has been successfully used for long-term wireless neural recording in freely behaving rhesus monkey.
A Distance-Based Locally Informed Particle Swarm Model for Multimodal Optimization

Multimodal optimization amounts to finding multiple global and local optima (as opposed to a single solution) of a function, so that the user can have a better knowledge about different optimal solutions in the search space and when needed, the current solution may be switched to a more suitable one while still maintaining the optimal system performance. Niching particle swarm optimizers (PSOs) have been widely used by the evolutionary computation community for solving real-parameter multimodal optimization problems. However, most of the existing PSO-based niching algorithms are difficult to use in practice because of their poor local search ability and requirement of prior knowledge to specify certain niching parameters. This paper has addressed these issues by proposing a distance-based locally informed particle swarm (LIPS) optimizer, which eliminates the need to specify any niching parameter and enhance the fine search ability of PSO. Instead of using the global best particle, LIPS uses several local bests to guide the search of each particle. LIPS can operate as a stable niching algorithm by using the information provided by its neighborhoods. The neighborhoods are estimated in terms of Euclidean distance. The algorithm is compared with a number of state-of-the-art evolutionary multimodal optimizers on 30 commonly used multimodal benchmark functions. The experimental results suggest that the proposed technique is able to provide statistically superior and more consistent performance over the existing niching algorithms on the test functions, without incurring any severe computational burdens.
Redox-sensitive homodimerization of Pex11p: a proposed mechanism to regulate peroxisomal division

Pex11p (formerly Pmp27) has been implicated in peroxisomal proliferation (Erdmann, R., and G. Blobel. 1995. J. Cell Biol. 128; 509- 523; Marshall, P.A., Y.I. Krimkevich, R.H. Lark, J.M. Dyer, M. Veenhuis, and J.M. Goodman, 1995. J. Cell Biol. 129; 345-355). In its absence, peroxisomes in Saccharomyces cerevisiae fail to proliferate in response to oleic acid; instead, one or two large peroxisomes are formed. Conversely, overproduction of Pex11p causes an increase in peroxisomal number. In this report, we confirm the function of Pex11p in organelle proliferation by demonstrating that this protein can cause fragmentation in vivo of large peroxisomes into smaller organelles. Pex11p is on the inner surface of the peroxisomal membrane. It can form homodimers, and this species is more abundant in mature peroxisomes than in proliferating organelles. Removing one of the three cysteines in the protein inhibits homodimerization. This cysteine 3-->alanine mutation leads to an increase in number and a decrease in peroxisomal density, compared with the wild-type protein, in response to oleic acid. We propose that the active species is the "monomeric" form, and that the increasing oxidative metabolism within maturing peroxisomes causes dimer formation and inhibition of further organelle division.
Differentiation and Bone Resorption Role of CX3CL1/Fractalkine in Osteoclast

The recruitment of osteoclast precursors toward osteoblasts and subsequent cell-cell interactions are critical for osteoclast differentiation. Chemokines are known to regulate cell migration and adhesion. CX3CL1 (also called fractalkine) is a unique mem-brane-bound chemokine that has dual functions for cells expressing its receptor CX3CR1: a potent chemotactic factor in its soluble form and a type of efﬁcient cell adhesion molecule in its membrane-bound form. In this paper, we demonstrate a novel role of CX3CL1 in osteoblast-induced osteoclast differentiation. We found that osteoclast precursors selectively expressed CX3CR1, whereas CX3CL1 is expressed by osteoblasts. We conﬁrmed that soluble CX3CL1 induced migration of bone marrow cells containing osteoclast precursors, whereas immobilized CX3CL1 mediated ﬁrm adhesion of osteoclast precursors. Furthermore, a blocking mAb against CX3CL1 efﬁciently inhibited osteoclast differentiation in mouse bone marrow cells cocultured with osteoblasts. Anti-CX3CL1 also signiﬁcantly suppressed bone resorption in neonatal mice by reducing the number of bone-resorbing mature osteoclasts. Collectively, CX3CL1 expressed by osteoblasts plays an important role in osteoclast differentiation, possibly through its dual functions as a chemotactic factor and adhesion molecule for osteoclast precursors expressing CX3CR1.
The Immune Enhancement of Sodium Lauryl Sulfoacetate in Chickens

The purpose of this study is to investigate feasibility of sodium lauryl sulfoacetate (SLS) as an immunoadjuvant in chickens. After treating with 62.5, 125, 250, or 500 μg/mL SLS in vitro, lymphocyte proliferation assay of chicken peripheral blood mononuclear cells showed that the OD570 values of all experimental groups, as well as Con A-stimulated group, were significantly higher than that of the untreated control group. After injection with 1.0, 2.0, or 4.0 mg/kg of SLS for 3 consecutive days, chickens were vaccinated with an attenuated vaccine against Newcastle disease virus (NDV), and the immunoadjuvant effects of SLS were evaluated on the basis of immune organ index, antibody response, and CD4 +/CD8 + T-cell ratio. The results confirmed that SLS could enhance NDV-specific antibody response and increase CD4 +/CD8 + T-cell ratio in vivo. Furthermore, SLS could improve NDV-specific antibody response in thiamphenicol-treated chickens. These data indicate that SLS not only can improve humoral immune response but also reverse the immunosuppressive effect of thiamphenicol in chickens.
Netrin‐1 Is a Critical Autocrine/Paracrine Factor for Osteoclast Differentiation

Bone metabolism is a vital process that involves resorption by osteoclasts and formation by osteoblasts, which is closely regulated by immune cells. The neuronal guidance protein Netrin‐1 regulates immune cell migration and inflammatory reactions, but its role in bone metabolism is unknown. During osteoclast differentiation, osteoclast precursors increase expression of Netrin‐1 and its receptor Unc5b. Netrin‐1 binds, in an autocrine and paracrine manner, to Unc5b to promote osteoclast differentiation in vitro, and absence of Netrin‐1 or antibody‐mediated blockade of Netrin‐1 or Unc5b prevents osteoclast differentiation of both murine and human precursors. We confirmed the functional relationship of Netrin‐1 in osteoclast differentiation in vivo using Netrin‐1‐deficient (Ntn1‐/‐) or wild‐type (WT) bone marrow transplanted mice. Notably, Ntn1‐/‐ chimeras have markedly diminished osteoclasts, as well as increased cortical and trabecular bone density and volume compared with WT mice. Mechanistic studies revealed that Netrin‐1 regulates osteoclast differentiation by altering cytoskeletal assembly. Netrin‐1 increases regulator of Rho‐GEF subfamily (LARG) and repulsive guidance molecule (RGMa) association with Unc5b, which increases expression and activation of cytoskeletal regulators RhoA and focal adhesion kinase (FAK). Netrin‐1 and its receptor Unc5b likely play a role in fusion of osteoclast precursors because Netrin‐1 and DC‐STAMP are tightly linked. These results identify Netrin‐1 as a key regulator of osteoclast differentiation that may be a new target for bone therapies. © 2015 American Society for Bone and Mineral Research.
Left Ventricular Untwisting Rate by Speckle Tracking Echocardiography

Background— Recent studies validated the measurement of left ventricular (LV) untwisting rate (UR) by speckle tracking echocardiography. A few reports suggest that it may provide additional noninvasive insight into LV diastolic function. Methods and Results— Simultaneous echocardiographic imaging and LV pressure measurements (7F Millar catheters) were performed in 8 adult dogs. Loading conditions were altered by caval occlusion, whereas lusitropic state was changed by dobutamine and esmolol infusion. Inferior vena cava occlusion at all experimental stages (baseline, dobutamine, esmolol) led to a significant decrease (P⩽0.01) in LV end-systolic volume (ESV) and a significant increase in UR (P=0.03). The best relation was observed between LV UR and ESV (r=−0.8, P<0.001). The clinical study was conducted in 67 patients (age 57±17 years, 19 women) undergoing simultaneous right heart catheterization and echocardiographic imaging, with 20 healthy subjects as a control group. There were 34 patients with ejection fraction (EF) <50% (25±9%), and 33 patients with normal EF and diastolic dysfunction (64±7%). Patients with LV systolic dysfunction had a significantly lower UR (−55 &ogr;/s) in comparison with the control group (−89 &ogr;/s) and patients with normal EF (−104 &ogr;/s, P<0.05), and the determinants of LV UR were twist, ESV, and &tgr; (r2=0.83, P<0.001). In patients with diastolic dysfunction and normal EF, twist and ESV were the independent predictors (r2=0.71, P<0.001). Conclusions— LV UR is reduced in patients with depressed EF, but not in those with diastolic dysfunction and normal EF, and is primarily determined by twist and ESV.
Elucidation of the subunit orientation in CCT (chaperonin containing TCP1) from the subunit composition of CCT micro‐complexes

A collection of chaperonin containing TCP1 (CCT) micro‐complexes that are comprised of subsets of the constitutively expressed CCT subunits have been identified. These CCT micro‐complexes have mol. wts ranging from 120 to 250 kDa and are present in cells at lower abundance (<5%) as compared with intact CCT. Biochemical characterization of these micro‐complexes has shown that several are comprised of two different types of CCT subunit. Furthermore, it was observed that each subunit associates with only one or two other different types of subunit, suggesting that each subunit has fixed partners. This observation, together with CCT gene counting being concordant with the 8‐fold structural symmetry, is consistent with predictions derived from analysis of the primary structures of these subunits concerning inter‐subunit interactions, and implies a unique topology of the subunits constituting the torodial ring in CCT. The series of subunit–subunit association patterns determined from CCT micro‐complexes has provided information to infer, from the 5040 (7! factorial) combinatorial possibilities, one probable subunit orientation within the toroidal ring.
Pressure Waves and Tephra Dispersal from Volcanic Explosions: Models, Observations, and Instrumentation

Real-time study of erupting vents is important for both monitoring and scientific purposes; because direct in-situ study of erupting vents is impractical, our best tools for studying eruptions in real time involve monitoring eruptive products and waves that travel far from the volcano. The atmosphere is a particularly advantageous medium for studying propagation and transport of volcanic waves and products: acoustic waves pass through it with minimal scattering, particles follow predictable trajectories, and the atmospheric structure that affects both is well-monitored. Analyses of acoustic waves and tephra deposits can provide important information on eruptions including total explosive energy, volume, and fragmentation processes. Additionally, the hazards associated with these processes justify the need to understand and model them. Despite the apparent simplicity of volcanic-atmospheric phenomena, many open questions and difficulties remain. This dissertation aims to address some of the challenges and help develop a better understanding of volcanic-atmospheric phenomena. In this work, I discuss and demonstrate tools to improve our understanding of such phenomena. A general introduction to atmospheric physics and eruptive processes is provided in chapter 1. A particularly severe problem addressed by this dissertation is analysis of pressure waves from powerful volcanic explosions. Due to theoretical and numerical difficulties
Lack of regional selectivity during the progression of Parkinson disease: implications for pathogenesis.

BACKGROUND Dopamine terminal loss in the putamen of patients with Parkinson disease (PD) shows a regional heterogeneity, reflecting selective vulnerability of degenerating neurons to mechanisms of cell death. HYPOTHESIS If the same pathogenic mechanisms are responsible for the onset and progression of PD, the regional selectivity of dopamine cell loss will be the same throughout the course of the disorder. OBJECTIVE To investigate the regional selectivity of dopamine terminal loss during the progression of PD. PARTICIPANTS We studied 67 patients with PD and 20 healthy subjects using positron emission tomography with [(11)C](+/-)dihydrotetrabenazine (DTBZ). RESULTS Regional values of DTBZ binding potential (calculated as maximum specific binding [B(max)] divided by the equilibrium dissociation constant K(d)) against disease duration in the putamen of PD patients were best described by a multivariate exponential model with distinct parallel asymptotic values that were significantly (P<.001) different across 4 regions of the putamen. The extent of loss of DTBZ binding potential with disease progression during the clinical stage of PD (early vs late PD) was similar between the anterior (-33%, using early PD as the baseline) and posterior (-29%) putamen. In contrast, the extent of loss of DTBZ binding potential in early PD, which reflects the cumulated loss of DTBZ binding potential from the onset of the disorder (in healthy subjects vs those with early PD), was significantly (P<.001) lower in the posterior (-58%, using healthy subjects as the baseline) than the anterior (-42%) putamen. CONCLUSION To the extent that DTBZ positron emission tomography provides an accurate estimate of loss of dopamine neurons, our findings suggest that the mechanisms responsible for the progression of PD may not be the same as those responsible for its onset.
Triple control of relaxation: implications in cardiac disease.

EARLY DETECTION of impaired relaxation has been emphasized recently for the evaluation of global and regional ventricular function in patients with heart disease. Although early relaxation abnormalities have been found in various cardiac diseases, the underlying mechanisms are not as yet fully understood. Given the recent progress in our understanding of relaxation of the heart,' these mechanisms can now be discerned