Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture

ABSTRACT The nonstarter lactic acid bacterium Leuconostoc pseudomesenteroides is a species widely found in the dairy industry and plays a key role in the formation of aromatic compounds. Here, we report the first genome sequence of a dairy strain of Leuconostoc pseudomesenteroides, which is 2 Mb.
Percutaneous Lumbar Pedicle Screw Placement Aided by Computer-Assisted Fluoroscopy-Based Navigation: Perioperative Results of a Prospective, Comparative, Multicenter Study

Study Design. Institutional review board-approved, prospective, multicenter, comparative study. Objective. To assess the accuracy and utility of a computer-assisted fluoroscopic navigation method for percutaneous placement of lumbar pedicle screws compared with conventional fluoroscopic placement. Summary of Background Data. Recent reports indicate that cortical breaches during percutaneous pedicle screw placement can exceed 15%. Computed tomography (CT)- and fluoroscopy-based navigation systems may facilitate increased placement accuracy with reduced radiation exposure and operative times. Methods. Patients were alternately assigned to either the Guidance or Control group. The Guidance group underwent lumbar pedicle screw placement using the oblique visualization technique and computer-assisted fluoroscopic navigation. The Control group underwent lumbar pedicle screw placement per standard percutaneous technique aided by fluoroscopy alone. Baseline demographics, visual analog scale (VAS) pain scores, and American Spinal Injury Association scores were obtained preoperatively and in the immediate postoperative period. Fluoroscopy times and guidewire insertion times were recorded intraoperatively. All postoperative CT scans were reviewed by an independent spine surgeon to grade screw placement accuracy. Results. Forty-two patients (210 screws) were assigned to the Guidance group and 34 patients (152 screws) were assigned to the Control group. Use of Guidance resulted in reduced average fluoroscopy usage per pedicle [6.6 sec (SD = 5.1) vs. 9.6 sec (SD 6.2), P < 0.001] and more expedient placement of guidewires per pedicle [3.65 min (SD = 2.31) vs. 4.43 min (SD = 2.56), P = 0.003]. The Guidance group experienced less than half of the breach rate of the Control group (3.0% vs. 7.2%, P = 0.055) and reduced breach magnitudes. None of the breaches resulted in a corresponding neurological deficit or required revision. All patient-reported outcomes were significantly improved after surgery and there were no significant differences in average postoperative VAS scores between treatment groups. Conclusion. Use of Guidance reduces fluoroscopy and insertion times with increased accuracy compared with conventional fluoroscopic methods of percutaneous pedicle screw insertion.
Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens*

Uronate dehydrogenase from Agrobacterium tumefaciens (AtUdh) belongs to the short-chain dehydrogenase/reductase superfamily and catalyzes the oxidation of d-galacturonic acid and d-glucuronic acid with NAD+ as a cofactor. We have determined the crystal structures of an apo-form of AtUdh, a ternary form in complex with NADH and product (substrate-soaked structure), and an inactive Y136A mutant in complex with NAD+. The crystal structures suggest AtUdh to be a homohexamer, which has also been observed to be the major form in solution. The monomer contains a Rossmann fold, essential for nucleotide binding and a common feature of the short-chain dehydrogenase/reductase family enzymes. The ternary complex structure reveals a product, d-galactaro-1,5-lactone, which is bound above the nicotinamide ring. This product rearranges in solution to d-galactaro-1,4-lactone as verified by mass spectrometry analysis, which agrees with our previous NMR study. The crystal structure of the mutant with the catalytic residue Tyr-136 substituted with alanine shows changes in the position of Ile-74 and Ser-75. This probably altered the binding of the nicotinamide end of NAD+, which was not visible in the electron density map. The structures presented provide novel insights into cofactor and substrate binding and the reaction mechanism of AtUdh. This information can be applied to the design of efficient microbial conversion of d-galacturonic acid-based waste materials.
Exposure to hydrocarbons and renal disease: an experimental animal model.

The association between hydrocarbon exposure and chronic glomerulonephritis is still a controversial scientific issue. Recent epidemiological evidence suggests a role of exposure to hydrocarbons in the progression of glomerulonephritis towards chronic renal failure. The present experimental study on rats has been designed to assess the possible role of styrene in the progression of adriamycin (ADR) nephrosis, a well known model of renal fibrosis following nephrotic syndrome induced by ADR. Female Sprague-Dawley rats were exposed to styrene, 300 ppm, 6 h/day, 5 days/week for 12 weeks (group 1); treated with ADR, 2 mg/Kg, i.v. , twice on day 1 and day 15 of the study (group 2); Additional groups of animals received both the styrene and ADR treatments (group 3) or served as controls (group 4). The urinary excretion of total and single proteins (albumin, Retinol-Binding Protein (RBP), Clara Cell 16 Kd protein (CC16), fibronectin) was measured monthly, whereas histopathology and determinations requiring blood sampling were carried out at the end of the experiment. A progressive increase in total proteinuria, falling in the nephrotic range already by the 6th week was observed in ADR-treated groups. Styrene exposure caused up to a 3- to 5-fold increase as compared to controls. Co-exposure to ADR and styrene also resulted in a proteinuria much greater than that caused by ADR alone. The interactive effect of styrene and ADR was statistically significant for albuminuria and urinary fibronectin. A similar response was observed for glomerular filtration rate at the end of the experiment, styrene-exposed animals showing hyperfiltration as compared to their respective control group. At the end of the experiment, histopathological scoring for interstitial infiltration and fibrosis was also significantly higher in styrene-treated animals as compared to their respective control groups. In ADR-treated rats, low molecular weight proteinuria (l.m.w.p.) was only slightly affected, suggesting minimal tubular dysfunction associated with extensive tubular atrophy. However, styrene-exposed animals showed l.m. w.p. higher than their respective controls. In summary, in this animal model we were able to confirm both styrene-induced microproteinuria, mainly albuminuria and minor increases in l.m. w.p., observed among occupationally exposed workers and the role of hydrocarbon exposure as a factor accelerating the progression of renal disease suggested by epidemiological investigations in patients suffering from chronic renal disease. Whereas in rats exposed to styrene only, microproteinuria was stable over time and minor histopathological changes were noted at the end of the experiment, evidence of a role of solvent exposure in the progression of ADR nephropathy was obtained in terms of both renal dysfunction and interstitial fibrosis. The mechanistic basis of styrene-ADR interaction is unclear. However, experimental evidence is consistent with epidemiological findings suggesting the need to avoid solvent exposure in patients suffering from renal diseases.
Diarrhetic shellfish poisoning toxin esters in Danish blue mussels and surf clams

Until recently, little focus was given to the presence of diarrhetic shellfish poisoning (DSP) toxin esters in seafood products. However, during the last few years, the occurrence of a high percentage of esters of the total amount of DSP toxins present in some seafood products has been observed. Samples of Danish surf clams (Spisola spp.) and blue mussels (Mytilus edulis) from 1999–2004 were analysed by liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) for the presence of DSP toxin esters. The samples contained only okadaic acid and esters of okadaic acid. The level of total okadaic acid equivalents ranged from 224 to 2516 µg kg−1 in surf clams. The percentage of okadaic acid esters of the total okadaic acid equivalents ranged from 83 to 98%, mean 95%. The level of total okadaic acid equivalents ranged from 43 to 1631 µg kg−1 in blue mussels. The percentage of okadaic acid esters of the total okadaic acid equivalents ranged from 21 to 86%, mean 59%. The probability of a high percentage of okadaic acid esters seems to increase with higher amounts of total okadaic acid equivalents in the bivalves. The large prevalence of DSP toxin esters are of particular importance because of the increased use of chemical methods instead of mouse bioassay for the detection of DSP toxicity.
Oligodendrocytes Are Targets of HIV-1 Tat: NMDA and AMPA Receptor-Mediated Effects on Survival and Development

Myelin pallor in HIV+ individuals can occur very early during the disease process. While myelin damage might partly originate from HIV-induced vascular changes, the timing suggests that myelin and/or oligodendrocytes (OLs) may be directly affected. Histological (Golgi–Kopsch, electron microscopy) and biochemical studies have revealed an increased occurrence of abnormal OL/myelin morphology and dysregulated myelin protein expression in transgenic mice expressing the HIV-1 transactivator of transcription (Tat) protein. This suggests that viral proteins by themselves might cause OL injury. Since Tat interacts with NMDARs, we hypothesized that activation of NMDARs and subsequent disruption of cytoplasmic Ca2+ ([Ca2+]i) homeostasis might be one cause of white matter injury after HIV infection. In culture, HIV-1 Tat caused concentration-dependent death of immature OLs, while more mature OLs remained alive but had reduced myelin-like membranes. Tat also induced [Ca2+]i increases and Thr-287 autophosphorylation of Ca2+/calmodulin-dependent protein kinase II β (CaMKIIβ) in OLs. Tat-induced [Ca2+]i was attenuated by the NMDAR antagonist MK801, and also by the AMPA/kainate receptor antagonist CNQX. Importantly, both MK801 and CNQX blocked Tat-induced death of immature OLs, but only MK801 reversed Tat effects on myelin-like membranes. These results suggest that OLs can be direct targets of HIV proteins released from infected cells. Although viability and membrane production are both affected by glutamatergic receptor-mediated Ca2+ influx, and possibly the ensuing CaMKIIβ activation, the roles of AMPARs and NMDARs appear to be different and dependent on the stage of OL differentiation. SIGNIFICANCE STATEMENT Over 33 million individuals are currently infected by HIV. Among these individuals, ∼60% develop HIV-associated neurocognitive disorders. Myelin damage and white matter injury have been frequently reported in HIV patients but not extensively studied. Clinical studies using combined antiretroviral therapy (cART) together with adjunctive “anti-inflammatory” drugs show no improvement over cART alone, suggesting existence of injury mechanisms in addition to inflammation. In our studies, oligodendrocytes exhibited rapid increases in intracellular Ca2+ level upon HIV-1 transactivator of transcription (Tat) exposure. Thus, immature and mature oligodendrocytes can be direct targets of Tat. Since ionotropic glutamate receptor antagonists can partially or fully reverse the detrimental effects of Tat, glutamate receptors could be a potential therapeutic target for white matter damage in HIV patients.
Ether‐linked analogue of 2‐arachidonoylglycerol (noladin ether) was not detected in the brains of various mammalian species

2‐Eicosa‐5′,8′,11′,14′‐tetraenylglycerol (2‐AG ether, HU310, noladin ether) is a metabolically stable ether‐linked analogue of 2‐arachidonoylglycerol (2‐AG), an endogenous cannabinoid receptor ligand. 2‐AG ether has been used as a valuable experimental tool by a number of investigators. Recently, several groups reported that 2‐AG ether is present in mammalian brains. We examined in detail whether 2‐AG ether actually exists in the brains of various mammalian species. We found that 2‐AG ether is not present, at least in an appreciable amount, in the rat brain by gas chromatography‐mass spectrometry analysis and fluorometric high performance liquid chromatography analysis. The level of 2‐AG ether in the rat brain was below 0.2 pmol/g brain, if at all present. Similar results were obtained for the mouse brain, hamster brain, guinea‐pig brain and pig brain. The fact that 2‐AG ether was not detected in the brains of various mammalian species is consistent with the fact that an ether bond is formed through enzymatic replacement of the fatty acyl moiety of 1‐acyl dihydroxyacetone phosphate by a fatty alcohol, the resultant 1‐O‐alkyl dihydroxyacetone phosphate being a common intermediate of the biosynthesis of ether‐linked lipids in mammalian tissues. It is rather questionable whether 2‐AG ether is present in appreciable amounts in the brain and acts as an ‘endogenous’ cannabinoid receptor ligand.
A qualitative review of studies of diabetes preventive care among minority patients in the United States, 1993-2003.

OBJECTIVE To review existing data to determine whether ethnic disparities exist for diabetes-related preventive care among adults in the United States. STUDY DESIGN Literature review. METHODS We identified diabetes-related studies published between 1993 and 2003, using a reproducible search strategy. Studies were selected for review if there were ethnic comparisons or if data on a specific ethnic minority were reported. From these studies, we extracted data on commonly accepted diabetes-related preventive-care measures (testing for glycemia, eye examinations, foot examinations, lipid profile, influenza vaccination, nephropathy assessment, smoking-cessation counseling). The sources were US healthcare facilities, national survey samples, Veterans Affairs facilities, Medicare databases, and managed care data. RESULTS Thirty-six studies met our search criteria. Data were extracted on glycemia testing (15 studies), eye examination rates (27 studies), foot examination rates (18 studies), lipid-profile assessment (15 studies), percentage of patients receiving influenza vaccinations (8 studies), nephropathy assessment (7 studies), and counseling referrals for smoking cessation (4 studies). The majority of the data indicated that the rates of diabetes monitoring are generally low regardless of the population being studied. The major ethnic differences reported were lower rates of eye examination, influenza vaccination, and lipid-profile testing among Hispanics and African Americans than among non-Hispanic whites. CONCLUSIONS Despite the availability of evidence-based guidelines, rates of diabetes preventive care are low, particularly for some measures in ethnic minority groups. Additional data are needed to further elucidate these disparities.
Transmembrane orientation and receptor‐like structure of the Rhizobium meliloti common nodulation protein NodC

The 46.8‐kd NodC protein of Rhizobium meliloti is a membrane protein, essential for nodule formation. Gene fusions of nodC to a portion of the λ cI repressor gene were used to define the membrane‐anchor domain which is necessary for membrane insertion of the NodC protein into the membrane. The transmembrane orientation of NodC was confirmed by surface‐specific radiolabeling and proteolysis experiments. A highly hydrophobic transmembrane‐anchor domain was found near the carboxyl terminus, separating a large extracellular domain which contains an unusual cysteine‐rich cluster from a short putative intracellular domain. Cross‐linking studies showed that the NodC protein exists in the membrane probably as a dimer. The domain structure of the NodC protein shows striking similiarities with cell surface receptors. In nodules of various legumes a truncated form of the NodC protein was detected. The processed NodC was associated with the bacteroids and the amount of this protein increased during nodule development.
EFFECT OF OMEGA-3 PUFA RICH OIL SOURCES ON EGG PRODUCTION PERFORMANCE OF JAPANESE QUAIL

A study was conducted to assess the egg production performance in Japanese quail upon enrichment of quail diets with Omega-3 PUFA rich sources like fish oil and linseed oil, independently and simultaneously at 2 and 4 per cent levels. The biological experiment was carried out by using Japanese quail that were randomly allotted to seven treatment groups with three replicates having ten females in each replicate. Japanese quail were reared under cage system to study the effect of feeding fish and linseed oils on laying performance from 7 to 26 weeks of age. The birds were provided with diets by incorporating different levels of fish and linseed oils individually or in combination. All the birds were fed with experimental diet ad libitum and had free access to wholesome water throughout the experimental period. The results of this study revealed that Japanese quail layers in 2 per cent fish oil group (84.62 per cent) recorded the highest hen day egg production. However, significant difference (P<0.05) in hen housed egg production was observed during 7-10 weeks of experimental period. At the end of the study period, Japanese quail layers fed with 2 per cent fish oil (T2) (114.86 eggs) recorded the highest hen housed egg production when compared to control group (T1) (110.77 eggs ).
Secondary Myelofibrosis in the Naturel History of JAK2, MPL and CALR Mutated Myeloproliferative Neoplasms

The WHO classification of the Myeloprolferative Neoplasms (MPN) distinguishes Essential Thrombocythemia (ET), Polycythemia Vera (PV) and Primary Myelofibrosis (PMF). Myelofibrosis (MF) is not a disease because reticulin and collagen fibrosis are produced by polyclonal fibroblasts in response to cytokines released from the clonal granulocytic and megakaryocytic progenitor cells in myeloproliferative disorders (MPD) in patients with ET and PV. The Hannover and Cologne Bone Marrow classification defined chronic or primary megakaryocytic granulocytic myeloproliferation (PMGM) as the third distinct prefibrotic MPN without features of PV. Vainchenker (2005) discovered the JAK2V617F somatic mutation as the driver cause of ET, trilinear PV of erythrocytic, megakaryocytic and granulocytic myeloproliferation (EMGM) and myeloid neoplasia of the spleen with secondary MF. Prefibrotic JAK2V617F mutated ET comprises three phenotypes: normocellular ET, ET with PV features in blood and bone marrow (prodromal PV) and hypercellular ET with predominant megakaryocytic granulocytic myeloproliferation (EMGM or masked PV) and moderate splenomegaly. JAK2V617F mutated ET and PV are featured by medium sized to large (pleomorphic) megakaryocytes with only a few giant forms. JAK2 exon 12 mutated MPN usually present with idiopathic erythrocythemia or early PV. Bone marrow histology in MPL515 positive ET and MF show clustered small and giant megakaryocytes with hyperlobulated stag-horn-like nuclei in a normocellular bone marrow with no features of PV already described in 1988 (Thiele). Bone marrow histology in prefibrotic CALR mutated ET and MF is associated with PMGM and dominated by dense clusters of large immature megakaryocytes with hypolobulated bulky (cloude-like) hyperchromatic nuclei, which are never seen in JAK2V617F, JAK2 exon 12 and MPL515 mutated MPN. Disease burden in JAK2, MPL and CALR mutated MPN is best reflected by the degree of anemia, splenomegaly, mutation allele burden, bone marrow cellularity and myelofibrosis.
Bubble shape oscillations and the onset of sonoluminescence.

An air bubble trapped in water by an oscillating acoustic field undergoes either spherical or nonspherical pulsations depending on the strength of the forcing pressure. Two different instability mechanisms (the Rayleigh-Taylor instability and parametric instability) cause deviations from sphericity. Distinguishing these mechanisms allows an explanation of many features of recent experiments on single bubble sonoluminescence, and suggests methods for finding sonoluminescence in different parameter regimes.
IMPROVED FAST ADAPTIVE SUBSPACE TRACKING

A new subspace tracking algorithm which gives accurate estimates of ther largest singular values and corresponding left singular vectors of overlapping rectangular matrices is presented. This algorithm has evolved from the Fast Approximate Subspace Tracking (FAST) algorithm by Real, Tufts, and Cooley, but has significantly better accuracy and computational efficiency. When there are abrupt changes in data, or the data is changing rapidly, a rectangular window can often give better performance than an exponential window because it can limit exactly how much older data is included. Some methods for estimating the signal subspace dimension require the singular values of the strong subspace. This algorithm can update ther largest singular values and corresponding left singular vectors in O(nr), wheren is the number of channels and r is the dimension of the strong subspace that we are tracking. There are no assumptions made about the strong subspace, but the accuracy of our singular vector and singular value estimates is related to the separation between the strong ”signal” subspace and the weak ”noise” subspace, which is just the signal to noise ratio. In this paper we present, (a) why this algorithm works, (b) why it is fast, and (c) how to use it to track a strong subspace.
The Clinical Course and Prognosis of Patients With Essential Thrombocythemia Treated With Hydroxyurea and Low-Dose Aspirin in an 11-Year Follow-Up

Background: The main objective of this study was to determine the clinical course and prognosis in patients with essential thrombocythemia, treated with hydroxyurea and low-dose aspirin, and complications of treatment in a 12-year follow-up with a precise and regular control. Methods: In this study, 76 patients with high-risk essential thrombocytosis were retrospectively studied. Data obtained from initial examinations, sonography, complications, and treatment were analyzed. Results: The mean follow-up was 66.8 months (minimum, 3 months; maximum, 137 months). The mean age of patients was 46.9 years. The mean platelet count of patients at diagnosis and the last follow-up were 818,000/mm 3 and 422,000/mm 3 , respectively. In 60 patients, a gene mutation test for JAK2 V617F was performed and was reported as 36.7% positive. Nine patients had bleeding, two of whom were reported after treatment, and eight cases had thrombosis. Macrocytosis and myelofibrosis were seen in 32 and one cases, respectively. Moreover, no cases of leukemia or malignancy due to cytoreduction therapy were seen. One case of skin lesion was seen. Conclusion: A rapid diagnosis, accurate and regular control, and timely treatment can improve the quality of life and reduce morbidity and threatening complications. This study showed that complications using aspirin and hydroxyurea treatment are at the minimum level. J Hematol. 2016;5(4):117-122 doi: https://doi.org/10.14740/jh305w
Ion Pump‐Interacting Proteins: Promising New Partners

Abstract: The sorting and regulation of the Na,K and H,K‐ATPases requires that the pump proteins must associate, at least transiently, with kinases, phosphatases, scaffolding molecules, and components of the cellular trafficking machinery. The identities of these interacting proteins and the nature of their associations with the pump polypeptides have yet to be elucidated. We have begun a series of yeast two‐hybrid screens employing structurally defined segments of pump polypeptides as baits in order to gain insight into the nature and function of these interacting proteins.