Miracle-dz/UniFAR-FTUs huggingface dataset:
Kinetic Analysis of Competition Between Sulfate Reducers and Methanogens for Hydrogen in Sediments

The competition between sulfate-reducing and methanogenic bacteria for hydrogen was investigated in eutrophic lake sediments that contained low in situ sulfate concentrations and in sulfate-amended sediments. Sulfate reduction and methane production coexisted in situ in lake surface sediments (0 to 2 cm), but methane production was the dominant terminal process. Addition of 10 to 20 mM sulfate to sediments resulted in a decrease in the hydrogen partial pressure and a concomitant inhibition of methane production over time. Molybdate inhibition of sulfate reduction in sulfate-amended sediments was followed by an increase in the hydrogen partial pressure and the methane production rate to values comparable to those in sediments not amended with sulfate. The sulfate reducer population had a half-saturation constant for hydrogen uptake of 141 pascals versus 597 pascals for the methanogen population. Thus, when sulfate was not limiting, the lower half-saturation constant of sulfate reducers enabled them to inhibit methane production by lowering the hydrogen partial pressure below levels that methanogens could effectively utilize. However, methanogens coexisted with sulfate reducers in the presence of sulfate, and the outcome of competition at any time was a function of the rate of hydrogen production, the relative population sizes, and sulfate availability.
Identification of patterns of gray matter abnormalities in schizophrenia using source-based morphometry and bagging

Despite its reliable diagnosis, schizophrenia lacks an objective diagnostic test or a validated biomarker, which prevents a better understanding of this disorder. Structural magnetic resonance imaging (sMRI) has been vastly explored to find consistent abnormality patterns of gray matter concentration (GMC) in schizophrenia, yet we are far from having reached conclusive evidence. This paper presents a machine learning approach based on resampling techniques to find brain regions with consistent patterns of GMC differences between healthy controls and schizophrenia patients, these regions being detected by means of source-based morphometry. This work uses multi-site data from the Mind Clinical Imaging Consortium, which is composed of sMRI data from 124 controls and 110 patients. Our method achieves a better classification rate than other algorithms and detects regions with GMC differences between both groups that are consistent with several findings on the literature. In addition, the results obtained on data from multiple sites suggest that it may be possible to replicate these results on other datasets.
2-(4-Nitrophenoxy)benzoic acid: a three-dimensional hydrogen-bonded framework in a triclinic structure having Z' = 3.

The title compound, C(13)H(9)NO(5), crystallizes in space group P-1, with Z' = 3. The molecules are linked by O-H.O hydrogen bonds [H.O = 1.79-1.81 A, O.O = 2.625 (3)-2.648 (3) A and O-H.O = 172-176 degrees ] into two types of R(2)(2)(8) dimer, only one of which is centrosymmetric. An extensive series of soft hydrogen bonds, of C-H.O and C-H.pi(arene) types, links the dimers into a three-dimensional framework.
The SH2-domain-containing inositol 5-phosphatase (SHIP) limits the motility of neutrophils and their recruitment to wounds in zebrafish

Summary Neutrophil recruitment to sites of injury or infection is essential for host defense, but it needs to be tightly regulated to prevent tissue damage. Phosphoinositide 3-kinase (PI3K), which generates the phosphatidylinositol (3,4,5)-trisphosphate [PI(3,4,5)P3], is necessary for neutrophil motility in vivo; however, the role of SH2-domain-containing 5-inositol phosphatase (SHIP) enzymes, which hydrolyze PI(3,4,5)P3 to phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2], is not well understood. Here we show that SHIP phosphatases limit neutrophil motility in live zebrafish. Using real-time imaging of bioprobes specific for PI(3,4,5)P3 and PI(3,4)P2 in neutrophils, we found that PI(3,4,5)P3 and PI(3,4)P2 accumulate at the leading edge while PI(3,4)P2 also localizes to the trailing edge of migrating neutrophils in vivo. Depletion of SHIP phosphatases using morpholino oligonucleotides led to increased neutrophil 3D motility and neutrophil infiltration into wounds. The increase in neutrophil wound recruitment in SHIP morphants was rescued by treatment with low dose PI3K&ggr; inhibitor, suggesting that SHIP limits neutrophil motility by modulating PI3K signaling. Moreover, overexpression of the SHIP phosphatase domain in neutrophils impaired neutrophil 3D migration. Taken together, our findings suggest that SHIP phosphatases control neutrophil inflammation by limiting neutrophil motility in vivo.
Reproducibility and sensitivity of scanning laser Doppler flowmetry during graded changes in Po 2

AIMS/BACKGROUND Recently a commercially available scanning laser Doppler flowmeter has been produced, which provides two dimensional maps of the retinal perfusion. The aim of the present study was to investigate the reproducibility and the sensitivity of these measurements. METHODS 16 healthy subjects were randomised to inhale different gas mixtures of oxygen and nitrogen in a double blind crossover study. The following gas mixtures of oxygen and nitrogen were administered: 100% oxygen + 0% nitrogen, 80% oxygen + 20% nitrogen, 60% oxygen + 40% nitrogen, 40% oxygen + 60% nitrogen, 30% oxygen + 70% nitrogen, 20% oxygen + 80% nitrogen, 15% oxygen + 85% nitrogen, and 10% oxygen + 90% nitrogen. Retinal haemodynamic variables and systemic haemodynamics were measured during all inhalation periods. Recordings under resting conditions were performed three times to calculate intraclass coefficients. RESULTS In two subjects we did not obtain technically adequate results. A dose dependent change in retinal blood flow during graded oxygen breathing was observed (p < 0.001). During 100% oxygen breathing blood flow decrease was between 29% and 33%, whereas blood flow increase was between 28% and 33% during inhalation of 10% oxygen + 90% nitrogen. CONCLUSIONS Scanning laser Doppler flowmetry has an acceptable reproducibility and is appropriate for description of the effect of graded changes in Po 2 on retinal haemodynamics. The main problems with the system are the large zero offset, the fixation during retinal scanning, and the neglect of blood flow changes during the cardiac cycle.
Differentiation of spotted fever group rickettsiae by sequencing and analysis of restriction fragment length polymorphism of PCR-amplified DNA of the gene encoding the protein rOmpA

Currently, the genotypic identification of the spotted fever group (SFG) rickettsiae is based on restriction fragment length polymorphism analysis of PCR-amplified genes coding for the enzyme citrate synthase and the surface proteins rOmpA and rOmpB. A set of useful restriction endonucleases was found following comparison of Rickettsia rickettsii and R. prowazekii sequences. However, by using three PCR amplifications and four enzyme digestions with this set, it was impossible to differentiate between all of the known serotypes of the SFG rickettsiae. We amplified by PCR and sequenced using an automated laser fluorescent DNA sequencer a fragment of the gene encoding the protein rOmpA from 21 serotypes of the SFG rickettsiae. A 632-bp amplification product was obtained for most of the strains, although no product could be obtained by using R. akari, R. australis, R. helvetica, and R. bellii DNAs. We found a characteristic sequence for all strains studied except the two isolates of R. massiliae, isolates GS and Mtul. Using the software package BISANCE, we determined the restriction map of this fragment and identified five potentially useful endonucleases, RsaI, AluI, PstI, XbaI, and AvaII. We confirmed the computer analysis-derived profiles by PCR-restriction fragment length polymorphism analysis. The combination of the profiles obtained after digestion of the PCR product by RsaI and PstI allowed for the differentiation of 16 strains. The use of AluI and XbaI allowed for the characterization of R. parkeri and strain HA-91, respectively. R. africae and strain S were differentiated by AvaII digestion. Thus, using a single PCR amplification, we were able to differentiate all of the SFG rickettsiae whose ompA gene was amplified by PCR.
Analysis of electromagnetic torque in sinusoidal excited switched reluctance machines having DC bias in excitation

This paper investigates the average torque in the novel switched reluctance machine (SRM) excited by sinusoidal bipolar excitation with DC bias by employing the Fourier series and FE analysis. The optimal leading angle of phase current ahead of the inductance for producing maximum torque and the optimal ratio of AC to DC bias for maximum torque per copper loss are derived analytically from the first and second harmonic components of inductance (L1 and L2). Thus, with the optimal leading angle and optimal ratio of AC to DC bias an analytical approach to determine the optimal rotor pole arc can also be developed. It shows that when L1 and L2 are anti-phase, the optimal leading angle decreases as the ratio of AC to DC bias increases, but increases when L1 and L2 are in phase. The optimal leading angle and optimal ratio of AC to DC increase slightly with the increase of L2 to L1 ratio. The ratio of L2 to L1 is observed to be negative for small rotor pole arc, but positive for large rotor pole arc. The optimal ratio of AC to DC bias is determined by the amplitude of L2 to L1 ratio. The magnetic saturation makes the optimal leading angle less sensitive to the ratio of AC to DC bias. The similar torque capability can be achieved for the unipolar excitation and sinusoidal bipolar excitation with DC bias.
Comparing the performance of bipolar and unipolar switching frequency to drive DC-AC Inverter

The inverter is a device that is used as an interface between the photovoltaic energy and the grid. The harmonic and distortion of the output current, and efficiency of the inverter are the main issues. This paper presents a model of Sinusoidal Pulse Width Modulation (SPWM) methods of unipolar and bipolar inverters in MATLAB and Psim software. A numerical model of the LC filter is derived in order to design and test the DC-AC inverter. The SPWM control is created by comparing triangle signal (a carrier waveform) and a reference signal (a sine waveform) whose frequency is the desired frequency. The simple circuit is used to characterize the scheme of SPWM techniques in order to obtain the pure output voltage and reduce the harmonic component. Empirical results show that the unipolar switching scheme is used in widespread a commercial PV inverter in order to have the flexibility to choose a filter and reduce the harmonic components. The switching frequency of the Sunny Boy inverter is found around 15 kHz and its transformer is estimated. Unipolar switching SPWM is very useful in low switching frequency than bipolar switching SPWM. The output voltage and current in both techniques have been analyzed in frequency and time domains.
Critical care in resource-poor settings: Lessons learned and future directions*

Context:Critical care faces the same challenges as other aspects of healthcare in the developing world. However, critical care faces an additional challenge in that it has often been deemed too costly or complicated for resource-poor settings. This lack of prioritization is not justified. Hospital care for the sickest patients affects overall mortality, and public health interventions depend on community confidence in healthcare to ensure participation and adherence. Some of the most effective critical care interventions, including rapid fluid resuscitation, early antibiotics, and patient monitoring, are relatively inexpensive. Although cost-effectiveness studies on critical care in resource-poor settings have not been done, evidence from the surgical literature suggests that even resource-intensive interventions can be cost effective in comparison to immunizations and human immunodeficiency virus care. In the developing world, where many critically ill patients are younger and have fewer comorbidities, critical care presents a remarkable opportunity to provide significant incremental benefit, arguably much more so than in the developed world. Essential Considerations:Key areas of consideration in developing critical care in resource-poor settings include: Personnel and training, equipment and support services, ethics, and research. Strategies for training and retaining skilled labor include tying education to service commitment and developing protocols for even complex processes. Equipment and support services need to focus on technologies that are affordable and sustainable. Ethical decision making must be based on data when possible and on transparent articulated policies always. Research should be performed in resource-poor settings and focus on needs assessment, prognostication, and cost effectiveness. Future Directions:The development of critical care in resource-poor settings will rely on the stepwise introduction of service improvements, leveraging human resources through training, a focus on sustainable technology, ongoing analysis of cost effectiveness, and the sharing of context-specific best practices. Although prevention, public health, and disease-specific agendas dominate many current conversations in global health, this is nonetheless a time ripe for the development of critical care. Leaders in global health funding hope to improve quality and length of life. Critical care is an integral part of the continuum of care necessary to make that possible.
CD4+ T Lymphocytes with Constitutive CD40 Ligand in Preautoimmune (NZB × NZW)F1 Lupus-Prone Mice: Phenotype and Possible Role in Autoreactivity1

Lupus disease is marked by B lymphocyte hyperactivity and the production of Abs to dsDNA. The production of these anti-dsDNA Abs is T lymphocyte dependent. However, it is not clear how CD4+ T lymphocytes provide help for B lymphocytes to produce IgG anti-dsDNA Abs. One possible mechanism is suggested by studies showing that human patients with systemic lupus erythematosus and lupus mice have increased numbers of CD40 ligand (CD40L)+ T and B lymphocytes. The results described in this study reveal that young, clinically healthy lupus-prone New Zealand Black × New Zealand White F1 (BWF1) mice have naive CD4+ T cells with preformed CD40L. These cells contribute to a brisk response to immunization and to the production of anti-dsDNA Abs. In vitro experiments revealed that CD4+ T cells with preformed CD40L could, upon stimulation, provide antiapoptotic signals for B cells but could not induce proliferation or reduce activation threshold. These results suggest that the direct target cells for the effect of T cells with preformed CD40L in lupus may not be B lymphocytes.
Engineering of homologous recombination hotspots with AU-rich sequences in brome mosaic virus

Previously, we observed that crossovers sites of RNA recombinants clustered within or close to AU-rich regions during genetic recombination in brome mosaic bromovirus (BMV) (P. D. Nagy and J. J. Bujarski. J. Virol. 70:415-426, 1996). To test whether AU-rich sequences can facilitate homologous recombination, AU-rich sequences were introduced into parental BMV RNAs (RNA2 and RNA3). These insertions created a homologous RNA2-RNA3 recombination hotspot. Two other AU-rich sequences also supported high-frequency homologous recombination if a common sequence with high or average G/C content was present immediately upstream of the AU-rich element. Homologous RNA recombination did not require any additional sequence motifs or RNA structures and was position nonspecific within the 3' noncoding region. These results suggest that nucleotide content (i.e., the presence of common 5' GC-rich or moderately AU-rich and 3' AU-rich regions) is the important factor that determines the sites of homologous recombination. A mechanism that involves replicase switching during synthesis of positive-sense RNA strands is presented to explain the observed results.
Diagnostic Utility of WT1 Immunostaining in Ovarian Sertoli Cell Tumor

WT1, the Wilms tumor gene product, can be expressed in various tumors from different anatomic sites, including some types of ovarian tumors. Regarding the latter, most studies have focused on surface epithelial-stromal tumors in which serous carcinomas are usually positive and endometrioid carcinomas are negative. Very few studies have specifically investigated this marker in ovarian sex cord-stromal tumors; however, limited data in the literature suggest that WT1 may be frequently expressed in sex cord-stromal tumors. As pure Sertoli cell tumor can be in the histologic differential diagnosis of endometrioid tumors (particularly borderline tumor and carcinoma) and carcinoid, immunostaining for WT1 might be of diagnostic value. Immunohistochemical staining for WT1 was performed in 108 ovarian tumors: pure Sertoli cell tumor (n=26), endometrioid borderline tumor (n=25), classic well-differentiated endometrioid carcinoma (n=23), sertoliform endometrioid carcinoma (n=12), and carcinoid (n=22). Additionally, inhibin and calretinin immunostaining were performed in all cases of Sertoli cell tumor for purposes of comparing expression with WT1. Extent of immunostaining was scored on a 0 to 4+ semiquantitative scale, and immunohistochemical composite scores based on a combination of extent and intensity of immunostaining were calculated in positive cases (possible range, 1 to 12). Nuclear expression of WT1 was present in 96% of Sertoli cell tumors, 16% of endometrioid borderline tumors, 13% of classic well-differentiated endometrioid carcinomas, 25% of sertoliform endometrioid carcinomas, and 0% of carcinoids. In Sertoli cell tumors, expression was diffuse (>50% of positive cells) in all positive cases. When positive in the non-Sertoli cell tumors, the extent of expression tended to be focal to patchy (50% or less positive cells). In Sertoli cell tumors, inhibin and calretinin were expressed in 96% and 54% of cases, respectively. The extent of expression of inhibin tended to be diffuse, similar to WT1; however, the extent of immunostaining for calretinin tended to be focal to patchy. The immunohistochemical composite scores for WT1, inhibin, and calretinin were 11.2, 7.6, and 4.8, respectively. Coordinate patterns for the extent of expression of WT1, inhibin, and calretinin in pure Sertoli cell tumor showed that all 3 markers were positive in 54% of cases; however, 42% were positive for WT1 and inhibin but negative for calretinin. In cases positive for both WT1 and inhibin, expression of both markers was diffuse in 84% of cases, but WT1 was diffuse while inhibin was focal to patchy in 16% of cases. We conclude that ovarian Sertoli cell tumor should be added to the growing list of WT1-positive tumors. This marker is useful for the distinction of Sertoli cell tumor from endometrioid tumors and carcinoid. The diagnostic utility of WT1 in Sertoli cell tumor is similar to inhibin but better than that of calretinin.
Plasma pentosidine and total homocysteine levels in relation to change in common carotid intima-media area in the first year of dialysis therapy.

BACKGROUND Homocysteine and advanced glycation end-products (AGEs), which accumulate in chronic kidney disease (CKD), are recently proposed cardiovascular risk factors. In this study, we evaluated the association between changes in calculated intima media (cIM) area of the common carotid artery during the first year of dialysis therapy and plasma total homocysteine (tHcy) level as well as circulating AGEs such as plasma pentosidine level. METHODS We studied 63 CKD patients (38 males) aged 52 +/- 12 years at a time-point close to start of dialysis treatment and after 12 months of dialysis treatment (41 on peritoneal and 22 on hemodialysis). The tHcy and plasma pentosidine levels were measured by HPLC. Change in cIM area was evaluated by non-invasive B mode ultrasonography. Malnutrition was assessed by subjective global assessment (SGA). RESULTS At basal, 70% of the patients had carotid plaques, 32% had symptomatic CVD, 38% had malnutrition, 30% had inflammation (CRP > or = 1 mg/dl) and 23% had diabetes mellitus, respectively. At baseline, the mean plasma pentosidine levels were similar in the patients with and without carotid plaques (36 +/- 21 vs 36 +/- 19 pmol/mg albumin, respectively), whereas the median plasma tHcy was significantly lower in the patients with carotid plaques than in the patients without carotid plaques (32 +/- 21 vs 52 +/- 42 pmol/l, p < 0.01, respectively). The prevalence of hyperhomocysteinemia (tHcy level > 13.7 micromol/l) was 95%. In univariate analysis, the change in cIM area during the first year of dialysis was significantly correlated with basal plasma pentosidine level (p = 0.31, p = 0.01), but not with basal tHcy (p = -0.11). However, neither pentosidine nor tHcy levels were correlated with cIM area at basal or at 12 months. In a stepwise multiple regression model, age and plasma pentosidine content, but not the tHcy level, associated with changes in the cIM area. CONCLUSION Progression of atherosclerosis, as indicated by changes in carotid intima-media area during the course of dialysis treatment, was associated with pentosidine, but not with tHcy, levels at baseline in these CKD patients. This suggests that the accumulation of AGEs in CKD patients may have a role in the pathogenesis of CVD in these patients. Since almost all CKD patients have hyperhomocysteinemia, this finding, however, does not exclude a role ofhomocysteine as a risk factor for CVD in CKD patients.
Case study of practical applications of smart grid technologies

The simple truth to making the distribution grid smarter is to deploy communications and leverage advanced controls that are commonplace in substation automation, remedial action schemes, power management systems, and industrial closed-loop power automation. The untapped powerful information within the protection, control, and monitoring intelligent electronic devices (IEDs) can be leveraged. Dramatic distribution automation improvements are available by simply enabling and coordinating the unused automation capabilities of the numerous isolated IEDs already in service throughout the power system via distributed communications. These improvements automatically and rapidly isolate faults, restore power, monitor demand, and maintain and restore stability for more reliable generation, transmission, and delivery of electric power. By communicating with one another to accomplish tasks formerly done by humans or left undone, these IEDs observe the state of the power system, make educated decisions, and then take action to preserve the stability and performance of the grid. The smart grid is a collection of information sources and the automatic control systems that manage the delivery of power, understand the changes in demand, and react to it by managing demand response. This paper focuses on distribution-level protection and automation techniques illustrated with real-world case study examples.