Miracle-dz/UniFAR-FTUs huggingface dataset:
A Role for Iron in an Ancient Carbonic Anhydrase*

Since 1933, carbonic anhydrase research has focused on enzymes from mammals (α class) and plants (β class); however, two additional classes (γ and δ) were discovered recently. Cam, from the procaryote Methanosarcina thermophila, is the prototype of the γ class and the first carbonic anhydrase to be characterized from either an anaerobic organism or the Archaea domain. All of the enzymes characterized from the four classes have been purified aerobically and are reported to contain a catalytic zinc. Herein, we report the anaerobic reconstitution of apo-Cam with Fe2+, which yielded Cam with an effective kcat that exceeded that for the Zn2+-reconstituted enzyme. Mössbauer spectroscopy showed that the Fe2+-reconstituted enzyme contained high spin Fe2+ that, when oxidized to Fe3+, inactivated the enzyme. Reconstitution with Fe3+ was unsuccessful. Reconstitution with Cu2+, Mn2+, Ni2+, or Cd2+ yielded enzymes with effective kcat values that were 10% or less than the value for the Zn2+-reconstituted Cam. Cam produced in Escherichia coli and purified anaerobically contained iron with effective kcat and kcat/Km values exceeding the values for Zn2+-reconstituted Cam. The results identify a previously unrecognized biological function for iron.
Iron oxide nanoparticle-labeled rat smooth muscle cells: cardiac MR imaging for cell graft monitoring and quantitation.

PURPOSE To perform a quantitative analysis of anionic maghemite nanoparticle-labeled cells in vitro and determine the effect of labeling on signal intensity at magnetic resonance (MR) imaging. MATERIALS AND METHODS The study was approved by the institutional animal care and use committee at Hôpital Bichat. In vitro cell proliferation, iron content per cell, and MR signal intensity of cells were measured in agarose phantoms for 0-14 days of culture after labeling of rat smooth muscle cells with anionic maghemite nanoparticles. Next, iron oxide-labeled smooth muscle cells were injected into healthy hearts and hearts with ischemic injury in seven live Fisher rats. Ex vivo MR imaging experiments in excised hearts 2 and 48 hours after injection were performed with a 1.5-T medical imaging system by using T2-weighted gradient-echo and spin-echo sequences. Histologic sections were obtained after MR imaging. Correlation analyses between division factor of iron load and cell amplification factor and between 1/T2 and number of labeled cells or number of days in culture were performed by using linear regression. RESULTS Viability of smooth muscle cells was not affected by magnetic labeling. Transmission electron micrographs of cells revealed the presence of iron oxide nanoparticles in vesicles up to day 14 of culture. Intracellular iron concentration decreased in parallel with cell division (r2 = 0.99) and was correlated with MR signal intensity (r2 = 0.95). T2*-weighted MR images of excised rat hearts showed hypointense signal in myocardium at 2 and 48 hours after local injection of labeled cells. Subsequent histologic staining evidenced iron oxide nanoparticles within cells and confirmed the presence of the original cells at 2 and 48 hours after implantation. CONCLUSION Magnetic labeling of smooth muscle cells with anionic maghemite nanoparticles allows detection of cells with MR imaging after local transplantation in the heart.
Years in Review: Recent Progress in Cellular Allergology

This review highlights the recent key advances in the biology of CD4+ effector T cells, antigen-presenting cells, Th17 and T regulatory cells, as well as immediate effector cells, such as mast cells, basophils and eosinophils, which are critically contributing to the better understanding of the pathophysiology of allergic diseases and are helping to improve their diagnosis and therapy. Some of the key advances with a direct impact on allergic asthma research and treatment are summarized.
Hearing thresholds in sickle cell anemia patients: emerging new trends?

PURPOSE OF STUDY Advances in medicine resulting in better understanding of sickle cell disease and general improvement of the well-being of the sufferers even in the developing countries have positively affected the dreadful outlook of this disease with resultant increase in the population of sickle cell disease patients reaching adulthood, and less severe complications. We therefore set out to evaluate the presence and severity of sensorineural hearing loss in sickle cell anemia (SCA) patients in the light of the overall improvement in the morbidity and mortality. METHODS A prospective case control study of SCA patients attending our adult SCA clinic and control subjects from homozygous hemoglobin AA patients attending the staff clinic of the hospital for routine medical tests. Tympanometry and diagnostic audiometry were performed on each patient. MAIN FINDINGS Forty-six SCA patients (21 males, 45.7%) aged 16-48 years with a mean age of 22.9 years +/- 6.45 and 42 controls (24 males, 57.1%) aged 15-39 years with a mean age of 23.7 years +/- 5.69 were included in this study. The average hearing thresholds of SCA patients were consistently higher than controls in all frequencies tested in both right and left ears. Of the 92 ears of SCA patients tested, 95.7% exhibited hearing thresholds within normal limits, and 4.3% had mild hearing loss. The controls had thresholds within normal limits. CONCLUSION The incidence of significant sensorineural hearing loss in SCA seems to have reduced in line with the general improvement and survival of SCA patients. The hearing loss is worse in the right ear and has a female preponderance. We hope that more aggressive primary and secondary prevention and adequate treatment of sickle cell crisis would reduce if not eliminate the hearing loss found in SCA.
Single-Phase On-Board Bidirectional PEV Charger for V2G Reactive Power Operation

This paper presents the design and implementation of a single-phase on-board bidirectional plug-in electric vehicle (PEV) charger that can provide reactive power support to the utility grid in addition to charging the vehicle battery. The topology consists of two-stages: a full-bridge ac-dc boost converter; and a half-bridge bidirectional dc-dc converter. The charger operates in two quadrants in the active-reactive power (PQ) power plane with five different operation modes (i.e., charging-only, charging-capacitive, charging-inductive, capacitive-only, and inductive-only). This paper also presents a unified controller to follow utility PQ commands in a smart grid environment. The cascaded two-stage system controller receives active and reactive power commands from the grid, and results in line current and battery charging current references while also providing a stable dynamic response. The vehicle's battery is not affected during reactive power operation in any of the operation modes. Testing the unified system controller with a 1.44 kVA experimental charger design demonstrates the successful implementation of reactive power support functionality of PEVs for future smart grid applications.
On the Analysis of Co-Occurrence of Anti-Patterns and Clones

In software engineering, a smell is a part of a software system’s source code with a poor quality and that may indicate a deeper problem. Although many kinds of smells have been studied to analyze their causes, their behavior, and their impact on software quality, those smells typically are studied independently from each other. However, if two smells coincide inside a class, this could increases their negative effect (e.g., spaghetti code that is being cloned across the system). In this paper we report results from an empirical study conducted to examine the relationship between two specific kinds of smells: code clones and antipatterns. We conducted our study on three open-source software systems: Azureus, Eclipse, and JHotDraw. Results show that between 32% and 63% of classes in the analysed systems present co-occurrence of smells, and that such classes are more risky in term of fault-proneness.
Deep Air : Forecasting Air Pollution in Beijing , China

Air pollution in urban environments has risen steadily in the last several decades. Such cities as Beijing and Delhi have experienced rises to dangerous levels for citizens. As a growing and urgent public health concern, cities and environmental agencies have been exploring methods to forecast future air pollution, hoping to enact policies and provide incentives and services to beneﬁt their citizenry. Much research is being conducted in environmental science to generate deterministic models of air pollutant behavior; however, this is both complex, as the underlying molecular interactions in the atmosphere need to be simulated, and often inaccurate. As a result, with greater computing power in the twenty-ﬁrst century, using machine learning methods for forecasting air pollution has become more popular. This paper investigates the use of the LSTM recurrent neural network (RNN) as a framework for forecasting in the future, based on time series data of pollution and meteorological information in Beijing. Due to the sequence dependencies associated with large-scale and longer time series datasets, RNNs, and in particular LSTM models, are well-suited. Our results show that the LSTM framework produces equivalent accuracy when predicting future timesteps compared to the baseline support vector regression for a single timestep. Using our LSTM framework, we can now extend the prediction from a single timestep out to 5 to 10 hours into the future. This is promising in the quest for forecasting urban air quality and leveraging that insight to enact beneﬁcial policy.
Melanoma without a Detectable Primary Site with Metastases to Lymph Nodes

OBJECTIVE To compare outcomes of patients with clinical nodal melanoma metastases that occurred without a detectable primary tumor (melanoma of unknown primary site; MUP) with those with a known primary site (KPM). METHODS We included data from 459 consecutive patients treated from 1994 to 2007 with radical therapeutic lymph node dissection (LND; stage IIIB, C) due to clinically palpable and pathologically confirmed lymph node metastases (229 axillary; 230 ilioinguinal). The median follow‐up was 49 months. RESULTS LND was performed in 59 cases (12.9%; 29 men, 30 women) due to MUP nodal metastases, including 33 axillary (14.4%) and 26 ilioinguinal (11.3%). In the MUP group, the 3‐ and 5‐year survival rates were 48% and 41%, respectively. Similar rates were observed in patients with KPM, even with matched‐pair analyses. Established prognostic factors (number of metastatic nodes, p=.005; extracapsular extension of metastases, p=.002) influenced survival in the MUP group. Relapses occurred in 31 (53%) and 299 (74.7%) cases in the MUP and KPM groups, respectively. CONCLUSIONS Survival rates in the MUP and KPM groups were similar, and the same prognostic factors affected both. Thus, all MUP cases should be treated as standard stage III melanomas. The authors have indicated no significant interest with commercial supporters.
Effects of teacher professional learning activities on student achievement growth

ABSTRACT The authors examined the effects of six types of teacher professional learning activities on student achievement growth over 4 years using statewide longitudinal survey data collected from 467 middle school mathematics teachers in 91 schools merged with 11,192 middle school students' mathematics scores in a standardized assessment in Missouri. The data showed that teacher-centered collaborative activities to learn about mathematics teaching and learning (teacher collaboration and informal communication) seem to be more effective in improving student mathematics achievement than learning activities that do not necessarily involve such teacher-centered collaborative opportunities (professional development programs, university courses, individual learning activities). Teacher-driven research activities through professional conference presentation and participation were also found to be associated with student achievement growth in mathematics. The districts and schools may benefit from investing their professional development funds and resources in facilitating teacher-centered collaborative and research-based learning activities in order to improve student learning.
Overexpression of the Ikaros  6 isoform is restricted to t(4;11) acute lymphoblastic leukaemia in children and infants and has a role in B‐cell survival

The Ikaros transcription factor has been shown to play an important role in the differentiation of both myeloid and lymphoid lineages. Mice heterozygous for a dominant negative (DN) ikaros isoform develop T‐cell leukaemia and lymphoma with 100% penetrance. Overexpression of DN Ikaros isoforms has been reported in some forms of leukaemia, such as childhood acute myelomonocytic and monocytic leukaemias, adult B‐cell acute lymphoblastic leukaemias (B ALL) and in childhood and adult pre‐B ALL. In this study, the expression of Ikaros isoforms in 49 infant and childhood leukaemia patients was analysed by reverse transcription polymerase chain reaction and Western blot analysis. We found overexpression of the DN Ikaros 6 (Ik6) isoform in a subset of leukaemia patients harbouring t(4;11) translocations. To further study the consequences of Ik6 overexpression in B ALL, we inducibly expressed Ik6 in BaF3 cells and found that Ik6 overexpression delayed cell death after interleukin‐3 withdrawal, suggesting that overexpression of Ik6 found in t(4;11) B cells could contribute to leukaemogenesis by preventing the apoptosis of cells in an environment with reduced survival factors.
DSP-specific field-programmable VLSI and its CAD environment

A field-programmable VLSI processor (FPVLSI) is proposed based on a bit-serial pipeline architecture and a mesh network that greatly reduce complexity of a programmable interconnection network. An area-efficient shift-register-based cell is also proposed based on regularity of bit-serial operation. To minimize an inter-cell network, functionality of a programmable switch block is realized only by programming cells. Moreover, direct allocation of a control/data flow graph (CDFG) is introduced to localize data transfer. As a result, an ultra-highly-parallel cellular array is achieved that can efficiently exploit high parallelism of DSP applications. The FPVLSI is designed in a 0.18mum CMOS design rule. Its performance at 700MHz is 4.7 to 9 times higher than that of a conventional FPGA in typical applications under constraints of the same chip area and the same power consumption
Neuropeptide Y inhibits axonal transport of particles in neurites of cultured adult mouse dorsal root ganglion cells

Neuropeptide Y (NPY) plays a modulatory role in processing nociceptive information. The present study investigated the effects of NPY on axonal transport of particles in neurites of cultured adult dorsal root ganglion (DRG) cells using video‐enhanced microscopy. Application of NPY decreased the number of particles transported in both the anterograde and retrograde directions. This effect was persistently observed during NPY application and was reversed after washout. The inhibitory effect of NPY was concentration dependent between 10−9m and 10−6m. The instantaneous velocity of individual particles moving in anterograde and retrograde directions was also reduced by NPY. Both the NPY Y1 receptor agonist [Leu31,Pro34]‐NPY and NPY Y2 receptor agonist NPY13‐36 mimicked the effect of NPY on the number of transported particles. An immunocytochemical study using an antiserum against the NPY Y1 receptor protein revealed that the Y1 receptor was expressed in the majority (85.9 %) of cultured adult mouse DRG cells. Pre‐treatment of cells with pertussis toxin, a GTP‐binding protein (G protein) inhibitor, completely blocked the inhibitory effect of NPY. Each application of SQ‐22536, an adenylate cyclase inhibitor, and H‐89, a protein kinase A inhibitor, mimicked and occluded the effect of NPY. In contrast, dibutyryl cAMP (dbcAMP), a membrane permeable cAMP analogue, and forskolin, an activator of adenylate cyclase, produced a transient increase in axonal transport. The application of dbcAMP and forskolin in combination with NPY negated the effect of NPY alone. These results suggest that NPY, acting at Y1 and Y2 receptors, inhibits axonal transport of particles in sensory neurones. The effect seems to be mediated by a pertussis toxin‐sensitive G protein, adenylate cyclase, and protein kinase A pathway. Therefore, NPY may be a modulatory factor for axonal transport in sensory neurones.
Gifted High-School Students' Perspectives on the Development of Perfectionism

Through the use of in-depth interviews, this study investigated how gifted high-school students scoring high on at least one measure of perfectionism (self-oriented, socially prescribed, or other-oriented) perceived their perfectionism as developing. Findings suggested support for three family history models outlined by Flett, Hewitt, Oliver, and Macdonald (2002). Lack of challenge in their early academic experiences was also indicated as an influence. Findings are discussed within the context of the current literature on perfectionism in gifted students, and avenues for future research are suggested.
Total Ionizing Dose Effects on hBN Encapsulated Graphene Devices

The constant-voltage electrical stress and 10-keV X-ray irradiation responses of encapsulated graphene-hBN devices are evaluated. Both constant-voltage stress and X-ray exposure induce only modest shifts in the current and the Dirac point of the graphene. Charge trapping at or near the graphene/BN interface is observed after X-ray irradiation. The experimental results suggest that net hole trapping occurs in the BN at low doses and that net electron trapping occurs at higher doses. First-principles calculations also demonstrate that hydrogenated substitutional carbon impurities at B/N sites at or near the graphene/BN interface can play an additional role in the radiation response of these structures.
Pediatric liver transplantation for primary sclerosing cholangitis

Primary sclerosing cholangitis (PSC) is a rare cholestatic liver disease in children. The aim of this study was to determine the characteristics and outcomes of children with PSC who were listed for liver transplantation (LT). Children who underwent transplantation for PSC according to the Studies of Pediatric Liver Transplantation (SPLIT) registry were compared to age‐matched children with chronic liver disease who underwent transplantation for other indications. Seventy‐nine patients (2.6% of the SPLIT cohort) required LT for PSC. The mean duration of the post‐LT follow‐up was 36.6 ± 32.7 months. Ulcerative colitis and Crohn's disease were diagnosed before LT in 46.0% and 3.3% of the patients, respectively, and inflammatory bowel disease (IBD) was diagnosed after LT in another 9.8%. The mean age at LT was 12.6 ± 3.9 years, and the mean waiting time was 10.2 ± 12.9 months. The mean z scores for height and weight at LT were significantly lower for the PSC group versus the non‐PSC group. For the PSC group, the 1‐ and 5‐year patient survival rates were 98.7% and 86.6%, respectively, and the 1‐ and 5‐year graft survival rates were 93.0% and 76.1%, respectively. Intrahepatic biliary strictures in the first 6 months post‐LT and cholangitis in the first 30 days post‐LT were more common in the PSC group versus the non‐PSC group (3.8% versus 0.8% for intrahepatic biliary strictures, P = 0.03, and 5.1% versus 1.1% for cholangitis, P = 0.01). Recurrent PSC was diagnosed in 9.8% of the patients at a mean of 18.7 ± 13.8 months after LT. IBD was associated with an increased risk of death (log‐rank P = 0.01) and recurrent PSC (P = 0.02). Five years post‐LT, the mean aspartate aminotransferase level was 60 ± 45 IU/L, and the mean gamma‐glutamyltransferase level was 209 ± 302 IU/L; both levels were significantly higher than the levels for non‐PSC patients. In conclusion, children with PSC had patient and graft survival rates equaling those of age‐matched children who underwent transplantation for other indications. IBD was associated with worse outcomes. Recurrence was observed in 9.8%, and the PSC patients had higher mean liver enzyme levels 5 years post‐LT. Liver Transpl 17:925–933, 2011. © 2011 AASLD.
A note on antibiotic resistance in the bacterial flora of raw sewage and sewage-polluted River Tigris in Mosul, Iraq.

Polluted water samples collected from the River Tigris in the vicinity of a raw sewage outfall were examined for the incidence of antibiotic resistance among coliform bacteria on three occasions during 1983. Eighty percent or more of the coliform bacteria were resistant to one or more antibiotics. At the same time, raw sewage samples were examined for the incidence of antibiotic-resistant bacteria, and Escherichia coli, Pseudomonas spp. and Staphylococcus spp. were selected for sensitivity testing. Collectively, more than 90% of the 480 strains of the three organisms were resistant to one or more antibiotics. The minimal inhibitory concentration (MIC) of ampicillin for twenty-nine strains including coliforms, E. coli, Klebsiella sp. , Serratia sp. , Ps. aeruginosa, Pseudomonas sp. , Micrococcus sp. , Staph. aureus, Streptococcus faecalis and Bacillus sp. from raw sewage and polluted River Tigris water was determined and that for Ps. aeruginosa was 250 micrograms/ml. The high incidence of antibiotic-resistant bacteria in natural waters could be related to the widespread use of antibiotics in this locality.
Global Diversification Discount and Its Discontents: Self-selection Makes a World of Difference

The documented discount on globally diversified firms is often cited, but a correlation is not per se evidence that global diversification destroys firm value. Firms choose to globally diversify based on their firm attributes, some of which may be unobservable. Given these exogenous firm attributes, the decision to diversify globally is endogenous and self-selected. Using the same specifications save for the Heckman selection instrument, our results contradict past research that did not address endogeneity. We posit that the global premium should reflect the value of multinational operating flexibility. We use the 2008-2009 financial crisis as creating exogenous variation to permit a test for the positive change in firm valuation due to global diversification. During and after the 2008-2009 financial crisis, the premium associated with global diversification became larger and more significant than before the 2008-2009 financial crisis. The churn of subsidiaries entering and exiting countries increased dur.
Screening of bacterial strains for pectinolytic activity: characterization of the polygalacturonase produced by Bacillus sp

One hundred sixty eight bacterial strains, isolated from soil and samples of vegetable in decomposition, were screened for the use of citrus pectin as the sole carbon source. 102 were positive for pectinase depolymerization in assay plates as evidenced by clear hydrolization halos. Among them, 30% presented considerable pectinolytic activity. The cultivation of these strains by submerged and semi-solid fermentation for polygalacturonase production indicated that five strains of Bacillus sp produced high quantities of the enzyme. The physico-chemical characteristics, such as optimum pH of 6.0 - 7.0, optimum temperatures between 45oC and 55oC, stability at temperatures above 40oC and in neutral and alkaline pH, were determined.