Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategic Distribution of Protective Proteins within Bran Layers of Wheat Protects the Nutrient-Rich Endosperm1[C][W][OA]

Bran from bread wheat (Triticum aestivum ‘Babbler’) grain is composed of many outer layers of dead maternal tissues that overlie living aleurone cells. The dead cell layers function as a barrier resistant to degradation, whereas the aleurone layer is involved in mobilizing organic substrates in the endosperm during germination. We microdissected three defined bran fractions, outer layers (epidermis and hypodermis), intermediate fraction (cross cells, tube cells, testa, and nucellar tissue), and inner layer (aleurone cells), and used proteomics to identify their individual protein complements. All proteins of the outer layers were enzymes, whose function is to provide direct protection against pathogens or improve tissue strength. The more complex proteome of the intermediate layers suggests a greater diversity of function, including the inhibition of enzymes secreted by pathogens. The inner layer contains proteins involved in metabolism, as would be expected from live aleurone cells, but this layer also includes defense enzymes and inhibitors as well as 7S globulin (specific to this layer). Using immunofluorescence microscopy, oxalate oxidase was localized predominantly to the outer layers, xylanase inhibitor protein I to the xylan-rich nucellar layer of the intermediate fraction and pathogenesis-related protein 4 mainly to the aleurone. Activities of the water-extractable enzymes oxalate oxidase, peroxidase, and polyphenol oxidase were highest in the outer layers, whereas chitinase activity was found only in assays of whole grains. We conclude that the differential protein complements of each bran layer in wheat provide distinct lines of defense in protecting the embryo and nutrient-rich endosperm.
Comparative Analysis of Renal Protein Expression in Spontaneously Hypertensive Rat

Objective. Molecular mechanisms of nephrosclerosis caused by hypertension are not well known. Understanding changes in renal protein expression in hypertension may provide further information on how hypertension caused renal injury. Methods and Results. In the present study, we showed the protein expression profiles of the kidney in spontaneously hypertensive rats and Wistar-Kyoto rats using two-dimensional gel electrophoresis (2-DE). Differentially expressed protein spots were excised, underwent in-gel tryptic digestion, and were analyzed by MALDI-TOF MS. Eleven spots were identified. Of these identified spots, four spots were newly appeared, five spots up-regulated, and two spots down-regulated. The identified spots were mainly involved in energy metabolism, lipid transferring between membranes, and cell proliferation. Conclusions. The expression of many proteins have changed significantly in the kidney of spontaneously hypertensive rat. NADP+-dependent isocitrate dehydrogenase may be a candidate for further investigation of pathophysiological mechanisms of renal injury in hypertension.
Isolation and characterization of two benzene-derived hemoglobin adducts in vivo in rats.

The present study was aimed at the characterization of the major adducts formed by reaction of the metabolites of [14C]benzene with rat hemoglobin in vivo. Groups of 12-week-old male Fisher rats received i.p. injections of a single dose of 10 mmol/kg body weight or three equal daily subdoses of 3.3 mmol/kg body weight of [14C]benzene. High-performance liquid chromatographic analysis of strong acid hydrolysates of the [14C]benzene-modified globin indicated that the two major adducts in rats cochromatographed with synthetic S-(2,5-dihydroxyphenyl)cysteine and S-phenylcysteine. These adducts were converted to O,O'-S-tris-acetyl-3-thiol-hydroquinone and S-phenylthioacetate, which were then characterized by gas chromatography/mass spectrometry. The major radioactive adduct peaks accounted for 60-75% of the total radioactivity associated with rat globin. Characterization of the S-(2,5-dihydroxyphenyl)cysteine adduct provides evidence that p-benzoquinone is formed as a reactive metabolite of benzene. Formation of the S-phenylcysteine adduct indicates that benzene oxide and/or a hydroxycyclohexadienyl free radical is formed as an active intermediate upon i.p. injection of benzene into rats.
Prognosis and Prognostic Factors for Unexplained Subarachnoid Hemorrhage: Review of 84 Cases

OBJECTIVE We conducted a retrospective study to investigate the prognosis, possible prognostic factors, and long-term natural history of subarachnoid hemorrhage of unexplained cause. METHODS This report contains a retrospective analysis of data for 84 patients with subarachnoid hemorrhage of unknown cause who were monitored for 1 month to 9.5 years, with an average follow-up period of 5.6 years. We evaluated the associations between computed tomographic (CT) scan features, clinical grade, loss of consciousness during hemorrhage, ventricular ratio, angiographic spasm, complications (such as death resulting from ischemia, early rebleeding, late rebleeding, epilepsy, hydrocephalus, and fixed ischemic deficits), and outcomes, using a nonparametric, two-sample, Kolmogorov-Smirnov test. The &khgr;2 test was used to test the independence of two categorical variables. RESULTS CT class exhibited a significant association with clinical grade (&ggr; = 0.865, P = 0.006), loss of consciousness during hemorrhage (&ggr; = 0.69, P = 0.001), and ventricular ratio (&ggr; = 0.8175, P = 0.01) but a nonsignificant association with angiographic vasospasm (&ggr; = 0.21, P = 0.2). Death resulting from ischemic complications and fixed ischemic deficits were strongly associated with clinical grade (P = 0.003 and P = 0.008, respectively) but weakly associated with CT class (P = 0.06 and P = 0.084, respectively). Angiographic vasospasm was strongly associated only with fixed ischemic deficits among complications (P = 0.001). Clinical outcome was strongly positively associated with CT class (&ggr; = 0.685, P = 0.001), clinical grade (&ggr; = 0.81, P = 0.001), and ventricular ratio (&ggr; = 0.57, P = 0.002) but weakly positively associated with loss of consciousness during hemorrhage (&ggr; = 0.459, P = 0.0487) and angiographic vasospasm (&ggr; = 0.48, P = 0.04). CONCLUSION Our study confirms earlier studies reporting a good prognosis for survival, but it does not confirm the earlier statements regarding low morbidity rates. Although clinical grade and the presence and amount of subarachnoid blood on CT scans are the major prognostic factors related to the incidence of ischemic complications, clinical grade and CT class are also the main parameters, with ventricular ratio, indicating clinical outcomes for patients with subarachnoid hemorrhage of unknown cause.
Genetic fusions of subunit c in the F0 sector of H+-transporting ATP synthase. Functional dimers and trimers and determination of stoichiometry by cross-linking analysis.

The multicopy c subunit of the H+-transporting ATP synthase of Escherichia coli folds through the transmembrane F0 sector as a hairpin of two hydrophobic alpha-helices with the proton-translocating aspartyl-61 side chain centered in the second transmembrane helix. The number of subunits c in the F0 complex, which is thought to determine the H+-pumping/ATP stoichiometry, was previously not determined with exactness but thought to range from 9-12. The studies described here indicate that the exact number is 12. Based upon the precedent of the subunit c in vacuolar-type ATPases, which are composed of four transmembrane helices and seem to have evolved by gene duplication of an F0-type progenitor gene, we constructed genetically fused dimers and trimers of E. coli subunit c. Both the dimeric and trimeric forms proved to be functional. These results indicate that the total number of subunit c in F0 should be a multiple of 2 and 3. Based upon a previous study in which the oligomeric organization of c subunits in F0 was determined by cross-linking of Cys-substituted subunits (Jones, P. C. , Jiang, W., and Fillingame, R. H. (1998) J. Biol. Chem. 273, 17178-17185), we introduced Cys into the first and last transmembrane helices of subunit c monomers, dimers, and trimers and attempted to generate cross-linked products by oxidation with Cu(II)-(1,10-phenanthroline)2. Double Cys substitutions at two sets of positions gave rise to extensive cross-linked multimers. Multimers of the monomer that extended up to the position of c12 were correlated and calibrated with distinct cross-linked species of the appropriate doubly Cys-substituted dimers (i.e. c2, c4, . c12) and doubly Cys-substituted trimers (i.e. c3, c6, c9, c12). The results show that there are 12 copies of subunit c per F0 in E. coli, the exact number having both mechanistic and structural significance.
A controlled study of peripheral neuropathy after bariatric surgery

Background: Although peripheral neuropathy (PN) occurs after bariatric surgery (BS), a causal association has not been established. Objectives: To ascertain whether PN occurs more frequently following BS vs another abdominal surgery, to characterize the clinical patterns of PN, to identify risk factors for PN, and to assess if nerve biopsy provides pathophysiologic insight. Methods: Retrospective review identified patients with PN after BS. The frequency of PN was compared with that of an age- and gender-matched, retrospectively evaluated cohort of obese patients undergoing cholecystectomy. Results: Of 435 patients who had BS, 71 (16%) developed PN. Patients developed PN more often after BS than after cholecystectomy (4/126; 3%) (p < 0.001). The clinical patterns of PN were polyneuropathy (n = 27), mononeuropathy (n = 39), and radiculoplexus neuropathy (n = 5). Risk factors included rate and absolute amount of weight loss, prolonged gastrointestinal symptoms, not attending a nutritional clinic after BS, reduced serum albumin and transferrin after BS, postoperative surgical complications requiring hospitalization, and having jejunoileal bypass. Most risk factors were associated with the polyneuropathy group. Sural nerve biopsies showed prominent axonal degeneration and perivascular inflammation. Conclusions: Peripheral neuropathy (PN) occurs more frequently after bariatric surgery (BS) than after another abdominal surgery. The three clinical patterns of PN after BS are sensory-predominant polyneuropathy, mononeuropathy, and radiculoplexus neuropathy. Malnutrition may be the most important risk factor, and patients should attend nutritional clinics. Inflammation and altered immunity may play a role in the pathogenesis, but further study is needed.
Citizens as More Than Sensors, Citizens as Agents for Change.

How might we tap into citizens’ knowledge, context, and passion on social media to have them be much more than just sensors, but rather, agents of change? What would it take to be able to orchestrate citizens on social media to execute ambitious goals, e.g., creating new infrastructure to support the indoor navigation of the visually impaired? The main challenge that is blocking these type of interactions at scale is that citizens have heterogeneous knowledge and usually lack the skills needed to complete the work needed to reach the collective goals. To address this problem, I introduce a novel architecture conformed of Intelligent Civic Blocks that use machine learning to: 1) help citizens on social media to build at execution time the skills they need to complete work associated with the large-scale collective effort; 2) empower citizens to develop their creativity and entrepreneurship to propose creative solutions to build improved societies. In this talk, I will present case-studies showcasing how this proposed architecture can lead to collective action organized on social media in a range of areas (see Fig. 1 for an example). In difference to prior work that focused primarily on using citizens as simple sensors, this research pushes towards new intelligent systems that enable the orchestration of collective action on social media to create improved societies.
A concept-level approach in analyzing review readership for E-Commerce persuasive recommendation

A rapid development of E-Commerce platforms has allowed retailers to introduce online product recommendations to persuade consumers purchase decisions. Recommendations system in E-Commerce can be implemented through development of opinion review or feedback system. The visibility of opinion review as a persuasive communication tool in recommendation context has been proven as an important role in purchasing process, which then triggers much attention recently among research scholars. To expand the current discussion on persuasive potential of online review system, this paper aims to explore how the quality of text message may affects the persuasiveness of online recommendation. A concept-level approach will be used in analyzing text readability ease towards generating persuasive communication message. A theoretical model is proposed to measure the effect of review length based on number of concept review towards opinion review readership and its persuasive features. In order to validate the model, we applied basic readability measure of Gunning-Fox Index (FOG) to examine readability ease of opinion review to a dataset containing 1054 reviews extracted from Amazon.com product review. The interrelationship between concept-level analysis, review readership and its persuasive review is further discussed in this paper.
Molecular fMRI

Comprehensive analysis of brain function depends on understanding the dynamics of diverse neural signaling processes over large tissue volumes in intact animals and humans. Most existing approaches to measuring brain signaling suffer from limited tissue penetration, poor resolution, or lack of specificity for well-defined neural events. Here we discuss a new brain activity mapping method that overcomes some of these problems by combining MRI with contrast agents sensitive to neural signaling. The goal of this “molecular fMRI” approach is to permit noninvasive whole-brain neuroimaging with specificity and resolution approaching current optical neuroimaging methods. In this article, we describe the context and need for molecular fMRI as well as the state of the technology today. We explain how major types of MRI probes work and how they can be sensitized to neurobiological processes, such as neurotransmitter release, calcium signaling, and gene expression changes. We comment both on past work in the field and on challenges and promising avenues for future development. SIGNIFICANCE STATEMENT Brain researchers currently have a choice between measuring neural activity using cellular-level recording techniques, such as electrophysiology and optical imaging, or whole-brain imaging methods, such as fMRI. Cellular level methods are precise but only address a small portion of mammalian brains; on the other hand, whole-brain neuroimaging techniques provide very little specificity for neural pathways or signaling components of interest. The molecular fMRI techniques we discuss have particular potential to combine the specificity of cellular-level measurements with the noninvasive whole-brain coverage of fMRI. On the other hand, molecular fMRI is only just getting off the ground. This article aims to offer a snapshot of the status and future prospects for development of molecular fMRI techniques.
Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry

P pili are multisubunit fibers essential for the attachment of uropathogenic Escherichia coli to the kidney. These fibers are formed by the noncovalent assembly of six different homologous subunit types in an array that is strictly defined in terms of both the number and order of each subunit type. Assembly occurs through a mechanism termed “donor-strand exchange (DSE)” in which an N-terminal extension (Nte) of one subunit donates a β-strand to an adjacent subunit, completing its Ig fold. Despite structural determination of the different subunits, the mechanism determining specificity of subunit ordering in pilus assembly remained unclear. Here, we have used noncovalent mass spectrometry to monitor DSE between all 30 possible pairs of P pilus subunits and their Ntes. We demonstrate a striking correlation between the natural order of subunits in pili and their ability to undergo DSE in vitro. The results reveal insights into the molecular mechanism by which subunit ordering during the assembly of this complex is achieved.
Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method

I report herein two 2.0 ns (1.0 fs time step) MD simulations of two zinc complexes bridged by a hydroxide in phosphotriesterase (PTE) employing the nonbonded method and the cationic dummy atom method that uses virtual atoms to impose orientational requirement for zinc ligands. The cationic dummy atom method was able to simulate the four‐ligand coordination of the two zinc complexes in PTE. The distance (3.39 ± 0.07Å) between two nearby zinc ions in the time‐average structure of PTE derived from the MD simulation using the cationic dummy atoms matched that in the X‐ray structure (3.31 ± 0.001Å). Unequivocally, the time‐average structure of PTE was able to fit into the experimentally determined difference electron density map of the corresponding X‐ray structure. The results demonstrate the practicality of the cationic dummy atom method for MD simulations of zinc proteins bound with multiple zinc ions. In contrast, a 2.0 ns (1.0 fs time step) MD simulation using the nonbonded method revealed a striking difference in the active site between the X‐ray structure and the time‐average structure that was unable to fit into the density map of PTE. The results suggest that caution should be used in the MD simulations using the nonbonded method. Proteins 2001;45:183–189. © 2001 Wiley‐Liss, Inc.
8-Isoprostaglandin E2 Enhances Receptor-activated NFκB Ligand (RANKL)-dependent Osteoclastic Potential of Marrow Hematopoietic Precursors via the cAMP Pathway*

Lipid oxidation products promote atherosclerosis and may also affect osteoporosis. We showed previously that oxidized lipids including 8-isoprostaglandin E2 (isoPGE2) inhibit osteoblastic differentiation of preosteoblasts. Since osteoporosis is mediated both by decreased osteoblastic bone formation and by increased osteoclastic bone resorption, we assessed whether oxidized lipids regulate the osteoclastic potential of marrow hematopoietic cells. Treatment of marrow-derived preosteoclasts with isoPGE2 enhanced osteoclastic differentiation as evidenced by increased tartrate-resistant acid phosphatase (TRAP) activity and multinucleation, which were inhibited by calcitonin, and increased numbers of resorption pits. The enhanced osteoclastic differentiation by isoPGE2 was observed whether preosteoclasts were in coculture with stromal cells or in monoculture in the presence of receptor-activated NFκB ligand (RANKL) and macrophage colony-stimulating factor. Receptor antagonist studies suggest that isoPGE2 effects were mediated by prostaglandin receptor subtypes EP2/DP on preosteoclasts and subtype EP1 and thromboxane receptors on stromal/osteoblast cells. The enhanced TRAP activity was also inhibited by cAMP-dependent protein kinase inhibitors, and isoPGE2 elevated intracellular cAMP levels of preosteoclast monocultures. Other oxidized lipids also enhanced the TRAP activity of preosteoclast monocultures. These data suggest that isoPGE2 enhances osteoclastic differentiation of marrow preosteoclasts and that this regulation occurs via the cAMP-dependent protein kinase pathway.
Botulinum type A toxin complex for the relief of upper back myofascial pain syndrome: how do fixed-location injections compare with trigger point-focused injections?

OBJECTIVE This was a prospective, randomized, double-blind, placebo-controlled, 12-week, multicenter study to evaluate the efficacy and tolerability of fixed location injections of botulinum type A toxin (BoNT-A, Dysport) in predetermined injection sites in patients with myofascial pain syndrome of the upper back. DESIGN Patients with moderate-to-severe myofascial pain syndrome affecting cervical and/or shoulder muscles (10 trigger points, disease duration 6-24 months) and moderate-to-severe pain intensity were randomized to BoNT-A (N = 81) or saline (N = 72). INTERVENTION Patients received treatment into 10 predetermined fixed injection sites in the head, neck, and shoulder (40 units of BoNT-A per site or saline, a total of 400 units of BoNT-A). OUTCOME MEASURES The primary efficacy outcome was the proportion of patients with mild or no pain at week 5 (responders). Secondary outcomes included changes in pain intensity and the number of pain-free days per week. RESULTS At week 5, 49% (37/76) of BoNT-A patients and 38% (27/72) of placebo patients had responded to treatment (P = 0.1873). Duration of daily pain was reduced in the BoNT-A group compared with the placebo group from week 5, with statistically significant differences at weeks 9 and 10 (P = 0.04 for both). Treatment was well tolerated. CONCLUSION Fixed-location treatment with BoNT-A of patients with upper back myofascial pain syndrome did not lead to a significant improvement of the main target parameter in week 5 after treatment. Only in week 8 were significant differences found. Several secondary parameters, such as physicians' global assessment and patients' global assessment, significantly favored BoNT-A over placebo at weeks 8 and 12.
Deficiency in the Heat Stress Response Could Underlie Susceptibility to Metabolic Disease

Heat treatment (HT) effectively prevents insulin resistance and glucose intolerance in rats fed a high-fat diet (HFD). The positive metabolic actions of heat shock protein 72 (HSP72), which include increased oxidative capacity and enhanced mitochondrial function, underlie the protective effects of HT. The purpose of this study was to test the ability of HSP72 induction to mitigate the effects of consumption of a short-term 3-day HFD in rats selectively bred to be low-capacity runners (LCRs) and high-capacity runners (HCRs)—selective breeding that results in disparate differences in intrinsic aerobic capacity. HCR and LCR rats were fed a chow or HFD for 3 days and received a single in vivo HT (41°C, for 20 min) or sham treatment (ST). Blood, skeletal muscles, liver, and adipose tissues were harvested 24 h after HT/ST. HT decreased blood glucose levels, adipocyte size, and triglyceride accumulation in liver and muscle and restored insulin sensitivity in glycolytic muscles from LCR rats. As expected, HCR rats were protected from the HFD. Importantly, HSP72 induction was decreased in LCR rats after only 3 days of eating the HFD. Deficiency in the highly conserved stress response mediated by HSPs could underlie susceptibility to metabolic disease with low aerobic capacity.