Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial variations of community structures and methane cycling across a transect of Lei-Gong-Hou mud volcanoes in eastern Taiwan

This study analyzed cored sediments retrieved from sites distributed across a transect of the Lei-Gong-Hou mud volcanoes in eastern Taiwan to uncover the spatial distributions of biogeochemical processes and community assemblages involved in methane cycling. The profiles of methane concentration and carbon isotopic composition revealed various orders of the predominance of specific methane-related metabolisms along depth. At a site proximal to the bubbling pool, the methanogenic zone was sandwiched by the anaerobic methanotrophic zones. For two sites distributed toward the topographic depression, the methanogenic zone overlaid the anaerobic methanotrophic zone. The predominance of anaerobic methanotrophy at specific depth intervals is supported by the enhanced copy numbers of the ANME-2a 16S rRNA gene and coincides with high dissolved Fe/Mn concentrations and copy numbers of the Desulfuromonas/Pelobacter 16S rRNA gene. Assemblages of 16S rRNA and mcrA genes revealed that methanogenesis was mediated by Methanococcoides and Methanosarcina. pmoA genes and a few 16S rRNA genes related to aerobic methanotrophs were detected in limited numbers of subsurface samples. While dissolved Fe/Mn signifies the presence of anaerobic metabolisms near the surface, the correlations between geochemical characteristics and gene abundances, and the absence of aerobic methanotrophs in top sediments suggest that anaerobic methanotrophy is potentially dependent on iron/manganese reduction and dominates over aerobic methanotrophy for the removal of methane produced in situ or from a deep source. Near-surface methanogenesis contributes to the methane emissions from mud platform. The alternating arrangements of methanogenic and methanotrophic zones at different sites suggest that the interactions between mud deposition, evaporation, oxidation and fluid transport modulate the assemblages of microbial communities and methane cycling in different compartments of terrestrial mud volcanoes.
Efficacy of ultra short sub‐30 minute incubation of 5‐aminolevulinic acid photodynamic therapy in vitro

The estimated incidence of cutaneous squamous cell carcinoma (SCC) is 700,000 cases per year. In the US, SCC incidence is highest among fair skinned adults older than 50 years of age. Thus, as the population ages, the reported number of SCCs will likely increase in the future. Photodynamic therapy (PDT) is an FDA approved therapy for treatment of actinic keratoses (AKs), a precursor to cutaneous SCC lesions. The FDA approved incubation time of the photosensitizing agent 5‐aminolevulinic acid (ALA) is 14–18 hours. Recent studies have investigated short ALA incubation times of 1–3 hours with ALA and PDT demonstrating treatment success. Therefore, the question exists whether ALA incubation periods of less than 30 minutes are efficacious. Herein, we evaluate the efficacy of short ALA incubation periods by measuring apoptosis after 10, 15, and 20 minutes of ALA incubation.
Localization of phospholamban in smooth muscle using immunogold electron microscopy

Phospholamban, the putative regulator of the Ca2+-ATPase in cardiac sarcoplasmic reticulum, was immunolocalized in canine visceral and vascular smooth muscle. Gently disrupted tissues were labeled with an affinity-purified phospholamban polyclonal antibody and indirect immunogold, using preembedding techniques. The sarcoplasmic reticulum of smooth muscle cells was specifically labeled with patches of immunogold distributed in a nonuniform fashion, while the sarcolemma did not appear to contain any phospholamban. The outer nuclear envelopes were also observed to be heavily labeled with the affinity- purified phospholamban polyclonal antibody. These findings suggest that phospholamban may play a role in the regulation of cytoplasmic and intranuclear calcium levels in smooth muscle cells.
Crosstalk between Hsp70 molecular chaperone, lysosomes and proteasomes in autophagy-mediated proteolysis in human retinal pigment epithelial cells

The pathogenesis of age‐related macular degeneration involves chronic oxidative stress, impaired degradation of membranous discs shed from photoreceptor outer segments and accumulation of lysosomal lipofuscin in retinal pigment epithelial (RPE) cells. It has been estimated that a major part of cellular proteolysis occurs in proteasomes, but the importance of proteasomes and the other proteolytic pathways including autophagy in RPE cells is poorly understood. Prior to proteolysis, heat shock proteins (Hsps), agents that function as molecular chaperones, attempt to refold misfolded proteins and thus prevent the accumulation of cytoplasmic protein aggregates. In the present study, the roles of the Hsp70 molecular chaperone and proteasomal and lysosomal proteolytic pathways were evaluated in human RPE cells (ARPE‐19). The Hsp70 and ubiquitin protein levels and localization were analysed by Western blotting and immunofluorescense. Confocal and transmission electron microscopy were used to detect cellular organelles and to evaluate the morphological changes. Hsp70 levels were modulated using RNA interference and overexpression techniques. Cell viability was measured by colorimetric assay. The proteasome inhibitor MG‐132 evoked the accumulation of perinuclear aggregates positive for Hsp70, ubiquitin‐protein conjugates and the lysosomal membrane protein LAMP‐2. Interestingly, the hsp70 mRNA depletion significantly increased cell death in conjunction with proteasome inhibition. We found that the accumulation of lysosomes was reversible: a cessation of proteasome inhibition led to clearance of the deposits via a mechanism believed to include autophagy. The molecular chaperone Hsp70, proteasomes and autophagy have an important regulatory role in the protein turnover of human RPE cells and may thus open new avenues for understanding degenerative processes in retinal cells.
Exploring Pianist Performance Styles with Evolutionary String Matching

We propose novel machine learning methods for exploring the domain of music performance praxis. Based on simple measurements of timing and intensity in 12 recordings of a Schubert piano piece, short performance sequences are fed into a SOM algorithm in order to calculate 'performance archetypes'. The archetypes are labeled with letters and approximate string matching done by an evolutionary algorithm is applied to find similarities in the performances represented by these letters. We present a way of measuring each pianist's habit of playing similar phrases in similar ways and propose a ranking of the performers based on that. Finally, an experiment revealing common expression patterns is briefly described.
PRINCIPLES OF FREEZE‐DRYING

When a tissue or other hydrated biological material dries from the liquid state it suffers severe shrinkage, is often altered chemically, and becomes relatively insoluble. When preservation for subsequent use is desired, one or more of these changes renders the final product unusable. However, it is possible to circumvent these undesirable consequences of drying by carrying out the removal of water from the frozen rather than the liquid state. The many considerations involved in the initial freezing of biological material are discussed thoroughly elsewhere in this monograph. It is the purpose of this presentation to examine the mechanism by which the drying of a frozen specimen takes place and the practical techniques by which this can be done. Freeze-drying, in brief, is the removal of water from a specimen after it has been f ro~en . l -~ As opposed to the destructive effects of drying from the liquid state, freeze-drying, under proper conditions, permits the maintenance of three major specimen characteristics: morphology, solubility, and chemical integrity. These characteristics are individually discussed below. When a specimen is frozen, the free water is removed from it and concentrated into scattered ice crystals composed of pure water. The size and distribution of these crystals will depend upon the speed of freezing.4 Since the water is not actually removed from the specimen, there is no gross change in volume other than the slight expansion resulting from the crystallization of ice. If the water is then removed from the ice directly to the vapor phase by one of the techniques described below, the specimen may retain its structure exactly as it existed in the frozen state, save that the positions once occupied by ice crystals will be simply empty holes. Where preservation of gross structure only is desired, large ice crystals derived by slow freezing can be tolerated. Where histological integrity on the microscopic level is the goal, freezing must be as rapid as possible in order to minimize the extent of ice crystal artifacts. Solubility. Loss of solubility following drying from the liquid state can be blamed in part upon chemical alterations of the specimen, but probably to a greater extent upon reduction of effective surface area. A freeze-dried material that contains the many spaces remaining after sublimation of the ice crystals has a spongy structure and an effective large surface-to-volume ratio that facilitates resolvation. The freeze-drying of many pharmaceuticals is carried out primarily to obtain a readily soluble product. Chemical integrity. As water is removed from a specimen, all of its solutes are concentrated a t least to a saturated solution. This is obviously not a suitable milieu for many biological compounds or systems. Although freezing creates a similar dehydration and concentration, rapid denaturation can be avoided by virtue of the reduced reaction rates obtained a t low temperature. Consequently, if one can freeze a specimen without destroying the system to be
Identification and Expression of the CCAP Receptor in the Chagas’ Disease Vector, Rhodnius prolixus, and Its Involvement in Cardiac Control

Rhodnius prolixus is the vector of Chagas’ disease, by virtue of transmitting the parasite Trypanosoma cruzi. There is no cure for Chagas’ disease and therefore controlling R. prolixus is currently the only method of prevention. Understanding the physiology of the disease vector is an important step in developing control measures. Crustacean cardioactive peptide (CCAP) is an important neuropeptide in insects because it has multiple physiological roles such as controlling heart rate and modulating ecdysis behaviour. In this study, we have cloned the cDNA sequence of the CCAP receptor (RhoprCCAPR) from 5th instar R. prolixus and found it to be a G-protein coupled receptor (GPCR). The spatial expression pattern in 5th instars reveals that the RhoprCCAPR transcript levels are high in the central nervous system, hindgut and female reproductive systems, and lower in the salivary glands, male reproductive tissues and a pool of tissues including the dorsal vessel, trachea, and fat body. Interestingly, the RhoprCCAPR expression is increased prior to ecdysis and decreased post-ecdysis. A functional receptor expression assay confirms that the RhoprCCAPR is activated by CCAP (EC50 = 12 nM) but not by adipokinetic hormone, corazonin or an extended FMRFamide. The involvement of CCAP in controlling heartbeat frequency was studied in vivo and in vitro by utilizing RNA interference. In vivo, the basal heartbeat frequency is decreased by 31% in bugs treated with dsCCAPR. Knocking down the receptor in dsCCAPR-treated bugs also resulted in loss of function of applied CCAP in vitro. This is the first report of a GPCR knock-down in R. prolixus and the first report showing that a reduction in CCAPR transcript levels leads to a reduction in cardiac output in any insect.
Detection of HER2 Amplification in Breast Carcinomas: Comparison of Multiplex Ligation-Dependent Probe Amplification (MLPA) and Fluorescence In Situ Hybridization (FISH) combined with Automated Spot Counting

In this study the detection of HER2 gene amplification was evaluated using Fluorescence In Situ Hybridization (FISH; PathVysion) in comparison with Multiplex Ligation-dependent Probe Amplification (MLPA), a PCR based technique. These two methods were evaluated on a series of 46 formalin fixed paraffin embedded breast carcinomas, previously tested for protein overexpression by HercepTest (grouped into Hercep 1+, 2+ and 3+). HER2 gene amplification (ratio ≥ 2.0) by FISH was found in 9/10, 10/30 and 0/6 in IHC 3+, 2+ and 1+/0 cases, respectively. Digitalized automated spot counting performed with recently developed CW4000 CytoFISH software was 100% concordant with manual FISH scoring. Using MLPA 18/46 samples showed a clear HER2 amplification. Comparing MLPA and IHC showed the same results as for FISH and IHC. All but one FISH positive cases (18/19) were confirmed by MLPA for the presence of the gene amplification. The overall concordance of detection of Her2 gene amplification by FISH and MLPA was 98% (45/46). Furthermore, both the level of amplification and equivocal results correlated well between both methods. In conclusion, MLPA is a reliable and reproducible technique and can be used as an either alternative or additional test to determine HER2 status in breast carcinomas.
Analysis of DNA Damage Induced by Benzene through Electrochemical Impedance Spectroscopy

Glassy carbon substrate, multi‐walled carbon nanotubes and double stranded DNA was coated layer by layer to form an electrode. The electrode was exposed to benzene solution for 5 minutes. The layer by layer coated carbon electrode forms a viable platform for the immobilization of DNA that effectively promotes electron transfer between the DNA and electrode. The electrochemical impedance spectroscopy and cyclic voltammetry measurements was taken before and after the exposure. The effects of adsorption potential, DNA concentration and quantity of carbon nanotubes used for DNA immobilization were investigated on the voltammetric behavior of DNA. These findings could be used to design a biosensor with linear response to benzene.
Effect of Mo Concentration on Dynamic Recrystallization Behavior of Low Carbon Microalloyed Steels

Using a Gleeble 3500 thermo‐mechanical simulator, the dynamic recrystallization (DRX) behavior and mechanical properties of four low C, Nb−Ti‐containing micro‐alloyed steels with a Mo content ranging from 0 to 0.27 wt% were investigated. The effects of Mo content, deformation temperature and strain rate on the DRX parameters were quantified. The flow curves showed the typical signs of DRX over a wide range of deformation conditions. However, at higher strain rates (5 s−1) and/or lower deformation temperatures (below 1000°C), dynamic recovery was observed. It was shown that Mo has an effect on retarding DRX in micro‐alloyed steels, most likely due to the solute drag.
Missed Opportunities to Address Cardiovascular Disease Risk Factors amongst Adults Attending an Urban HIV Clinic in South Africa

We assessed cardiovascular disease (CVD) risk factor prevalence and risk stratification amongst adults on antiretroviral therapy in South Africa. Of the 175 patients screened, 37.8% had high blood pressure (HBP), 15.4% were current smokers, 10.4% had elevated cholesterol, and 4.1% had diabetes, but very few (3.6%) had a 10-year CVD risk >10%. One-third of those with HBP, 40% of those with diabetes, and two-thirds of those with high cholesterol had not previously been diagnosed. Although participants were adherent with chronic HIV care, screening for and management of CVDRF were suboptimal, representing a missed opportunity to reduce non-AIDS morbidity and mortality.
Trappin-2/Elafin Modulate Innate Immune Responses of Human Endometrial Epithelial Cells to PolyI∶C

Background Upon viral recognition, innate and adaptive antiviral immune responses are initiated by genital epithelial cells (ECs) to eradicate or contain viral infection. Such responses, however, are often accompanied by inflammation that contributes to acquisition and progression of sexually transmitted infections (STIs). Hence, interventions/factors enhancing antiviral protection while reducing inflammation may prove beneficial in controlling the spread of STIs. Serine antiprotease trappin-2 (Tr) and its cleaved form, elafin (E), are alarm antimicrobials secreted by multiple cells, including genital epithelia. Methodology and Principal Findings We investigated whether and how each Tr and E (Tr/E) contribute to antiviral defenses against a synthetic mimic of viral dsRNA, polyinosine-polycytidylic acid (polyI∶C) and vesicular stomatitis virus. We show that delivery of a replication-deficient adenovector expressing Tr gene (Ad/Tr) to human endometrial epithelial cells, HEC-1A, resulted in secretion of functional Tr, whereas both Tr/E were detected in response to polyI∶C. Moreover, Tr/E were found to significantly reduce viral replication by either acting directly on virus or through enhancing polyI∶C-driven antiviral protection. The latter was associated with reduced levels of pro-inflammatory factors IL-8, IL-6, TNFα, lowered expression of RIG-I, MDA5 and attenuated NF-κB activation. Interestingly, enhanced polyI∶C-driven antiviral protection of HEC-Ad/Tr cells was partially mediated through IRF3 activation, but not associated with higher induction of IFNβ, suggesting multiple antiviral mechanisms of Tr/E and the involvement of alternative factors or pathways. Conclusions and Significance This is the first evidence of both Tr/E altering viral binding/entry, innate recognition and mounting of antiviral and inflammatory responses in genital ECs that could have significant implications for homeostasis of the female genital tract.
Traumatic Brain Injury: Current Treatment Strategies and Future Endeavors.

Traumatic brain injury presents in various forms ranging from mild alterations of consciousness to an unrelenting comatose state and death. In the most severe form of traumatic brain injury, the entirety of the brain is affected by a diffuse type of injury and swelling. Treatment modalities vary extensively based on the severity of the injury and range from daily cognitive therapy sessions to radical surgery such as bilateral decompressive craniectomies. Guidelines have been set forth regarding the optimal management of traumatic brain injury, but they must be taken in context of the situation and cannot be used in every individual circumstance. In this review article, we have summarized the current status of treatment for traumatic brain injury in both clinical practice and basic research. We have put forth a brief overview of the various subtypes of traumatic injuries, optimal medical management, as well as both the non-invasive and invasive monitoring modalities, in addition to the surgical interventions necessary in particular instances. We have overviewed the main achievements in searching for therapeutic strategies of traumatic brain injury in basic science. We have also discussed the future direction for developing traumatic brain injury treatment from an experimental perspective.
Validation, repeatability and reproducibility of a noninvasive instrument for measuring thoracic and lumbar curvature of the spine in the sagittal plane.

BACKGROUND The need for early identification of postural abnormalities without exposing patients to constant radiation has stimulated the development of instruments aiming to measure the spinal curvatures. OBJECTIVE To verify the validity, repeatability and reproducibility of angular measures of sagittal curvatures of the spine obtained using an adapted arcometer, by comparing them with Cobb angles of the respective curvatures obtained by using X-rays. METHODS 52 participants were submitted to two procedures designed to evaluate the thoracic and lumbar curvatures: (1) X-ray examination from which the Cobb angles (CA) of both curvatures were obtained, and (2) measuring the angles with the arcometer (AA). Two evaluators collected the data using the arcometer, with the rods placed at T1, T12, L1 and L5 spinous processes levels in a way as to permit linear measurements which, with aid of trigonometry, supplied the AA. RESULTS There was a very strong and significant correlation between AA and CA (r=0.94; p<0.01), with no-significant difference (p=0.32), for the thoracic curvature. There was a strong and significant correlation for the lumbar curvature (r=0.71; p<0.01) between AA and CA, with no-significant difference (p=0.30). There is a very strong correlation between intra-evaluator and inter-evaluator AA. CONCLUSION It was possible to quantify reliably the thoracic and lumbar curvatures with the arcometer and it can thus be considered valid and reliable and for use in evaluating spinal curvatures in the sagittal plane.
Gene Expression of Growth Factors and Growth Factor Receptors for Potential Targeted Therapy of Canine Hepatocellular Carcinoma

ABSTRACT The purpose of this study was to evaluate the gene expression of growth factors and growth factor receptors of primary hepatic masses, including hepatocellular carcinoma (HCC) and nodular hyperplasia (NH), in dogs. Quantitative real-time reverse transcriptase-polymerase chain reaction was performed to measure the expression of 18 genes in 18 HCCs, 10 NHs, 11 surrounding non-cancerous liver tissues and 4 healthy control liver tissues. Platelet-derived growth factor-B (PDGF-B), transforming growth factor-α, epidermal growth factor receptor, epidermal growth factor and hepatocyte growth factor were found to be differentially expressed in HCC compared with NH and the surrounding non-cancerous and healthy control liver tissues. PDGF-B is suggested to have the potential to become a valuable ancillary target for the treatment of canine HCC.
Invariant Rules for Multipolarization SAR Change Detection

This paper deals with coherent (in the sense that both amplitudes and relative phases of the polarimetric returns are used to construct the decision statistic) multipolarization synthetic aperture radar (SAR) change detection assuming the availability of reference and test images collected from N multiple polarimetric channels. At the design stage, the change detection problem is formulated as a binary hypothesis testing problem, and the principle of invariance is used to come up with decision rules sharing the constant false alarm rate property. The maximal invariant statistic and the maximal invariant in the parameter space are obtained. Hence, the optimum invariant test is devised proving that a uniformly most powerful invariant detector does not exist. Based on this, the class of suboptimum invariant receivers, which also includes the generalized likelihood ratio test, is considered. At the analysis stage, the performance of some tests, belonging to the aforementioned class, is assessed and compared with the optimum clairvoyant invariant detector. Finally, detection maps on real high-resolution SAR data are computed showing the effectiveness of the considered invariant decision structures.