Miracle-dz/UniFAR-FTUs huggingface dataset:
Enriching rice with Zn and Fe while minimizing Cd risk

Enriching iron (Fe) and zinc (Zn) content in rice grains, while minimizing cadmium (Cd) levels, is important for human health and nutrition. Natural genetic variation in rice grain Zn enables Zn-biofortification through conventional breeding, but limited natural Fe variation has led to a need for genetic modification approaches, including over-expressing genes responsible for Fe storage, chelators, and transporters. Generally, Cd uptake and allocation is associated with divalent metal cations (including Fe and Zn) transporters, but the details of this process are still unknown in rice. In addition to genetic variation, metal uptake is sometimes limited by its bioavailability in the soil. The availability of Fe, Zn, and Cd for plant uptake varies widely depending on soil redox potential. The typical practice of flooding rice increases Fe while decreasing Zn and Cd availability. On the other hand, moderate soil drying improves Zn uptake but also increases Cd and decreases Fe uptake. Use of Zn- or Fe-containing fertilizers complements breeding efforts by providing sufficient metals for plant uptake. In addition, the timing of nitrogen fertilization has also been shown to affect metal accumulation in grains. The purpose of this mini-review is to identify knowledge gaps and prioritize strategies for improving the nutritional value and safety of rice.
Compiler-directed ILP extraction for clustered VLIW/EPIC machines: predication, speculation and modulo scheduling

Compiler-directed ILP extraction techniques are critical to effectively exploiting the significant processing capacity of contemporaneous VLIW/EPIC machines. In this paper we propose a novel algorithm for ILP extraction targeting clustered EPIC machines that integrates three powerful techniques: predication, speculation and modulo scheduling. In addition, our framework schedules and binds operations, generating actual VLIW code. To the best of our knowledge, there is no other algorithm in the literature on predicated code optimizations that jointly considers speculation and modulo scheduling in the context of clustered EPIC machines. Our experimental results show that by jointly considering different extraction techniques in a resource aware context, the proposed algorithm can take maximum advantage of the resources available on the clustered machine, aggressively improving performance.
Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools

Nontuberculous mycobacteria (NTM) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. Although most NTM are saprophytes, approximately one-third of NTM have been associated with human diseases. In this study, we did a comparative proteomic analysis among five NTM strains isolated from several sources. There were different numbers of protein spots from M. gordonae (1,264), M. nonchromogenicum type I (894), M. nonchromogenicum type II (935), M. peregrinum (806), and M. scrofulaceum/Mycobacterium mantenii (1,486) strains, respectively. We identified 141 proteins common to all strains and specific proteins to each NTM strain. A total of 23 proteins were selected for its identification. Two of the common proteins identified (short-chain dehydrogenase/reductase SDR and diguanylate cyclase) did not align with M. tuberculosis complex protein sequences, which suggest that these proteins are found only in the NTM strains. Some of the proteins identified as common to all strains can be used as markers of NTM exposure and for the development of new diagnostic tools. Additionally, the specific proteins to NTM strains identified may represent potential candidates for the diagnosis of diseases caused by these mycobacteria.
Homologous and nonhomologous rearrangements: Interactions and effects on evolvability

By using Aevol, a simulation framework designed to study the evolution of genome structure, we investigate the effect of homologous rearrangements on the course of evolution. We designed an efficient model of rearrangements based on an intermittent search algorithm. Then, using experimental in silico evolution, we explore the effect of rearrangement rates on the genome structure. We show that the effect of homologous rearrangements is quite complex. At first glance they appear to be dangerous enough to trigger an indirect selective pressure leading to short genomes when the rearrangement rate is high. However, by analyzing the successful lineage in the best runs, we found that there is a positive correlation between the number of homologous rearrangements and the fitness improvement in these lineages. Thus the impact of homologous rearrangements on evolution is rather complex: dangerous on the one hand but necessary on the other hand, to ensure a sufficient level of evolvability to the organisms. Moreover, our results show that the spontaneous rate of small mutations influences the relative proportions of homologous versus nonhomologous rearrangements.
Robust bi-stable memory operation in single-layer graphene ferroelectric memory

With the motivation of realizing an all graphene-based circuit for low power, we present a reliable nonvolatile graphene memory device, single-layer graphene (SLG) ferroelectric field-effect transistor (FFET). We demonstrate that exfoliated single-layer graphene can be optically visible on a ferroelectric lead-zirconate-titanate (PZT) substrate and observe a large memory window that is nearly equivalent to the hysteresis of the PZT at low operating voltages in a graphene FFET. In comparison to exfoliated graphene, FFETs fabricated with chemical vapor deposited (CVD) graphene exhibit enhanced stability through a bi-stable current state operation with long retention time. In addition, we suggest that the trapping/de-trapping of charge carriers in the interface states is responsible for the anti-hysteresis behavior in graphene FFET on PZT. V C 2011 American Institute of Physics. [doi:10.1063/1.3619816] Graphene is considered to be an exceptional material with high potential for future electronics, owing to its excellent electronic properties; 1 linear electron energy dispersion, and high room temperature mobility. If feasible, an all graphene-based circuit, including logic, analog, and memory devices, would be of great interest to further extend the performance of current Si-based electronics. Among various device applications, graphene based memory structures are still in their infancy in comparison to its logic and analog applications. To date, graphene memory has been demonstrated through chemical modification, 2 filament-type memristor, 3 nanomechanical switch, 4 and graphene FFETs. 5‐7 In graphene FFETs, however, the ambipolar conduction leads to undesirable on/off states for memory applications. Moreover, the absence of an electronic bandgap and controlled doping makes it difficult to resolve such issues. Therefore, a systematic study of graphene FFET is beneficial to realize graphene-based memory structures. In this Letter, we investigate graphene/PZT FFET structures using exfoliated- and CVD-SLG and their mechanism of operation. We show that exfoliated SLG can be optically identified on a PZT substrate and exhibit a hysteresis of the Vshaped conductance with a large memory window at low operating gate voltages. We compare exfoliated- with CVDSLG FFETs and show that devices made of CVD-SLG exhibit a robust bi-stable current state with a long retention time. In order to construct the SLG FFET, we first engineered a ferroelectric substrate to identify SLG. Previously, we have demonstrated that SLG is invisible under the optical micro
Identification of a Glycoprotein from Rat Liver Mitochondrial Inner Membrane and Demonstration of Its Origin in the Endoplasmic Reticulum*

Employing antisera against various subfractions of rat liver mitochondria (mitoplast, inner membrane, intermembrane, and matrix) as well as metabolically radiolabeled BRL-3A rat liver cells, we undertook a search for the presence of glycoproteins in this major cellular compartment for which little information in regard to glycoconjugates was available. Subsequent to [35S]methionine labeling of BRL-3A cells, a peptide:N-glycosidase-sensitive protein (45 kDa) was observed by SDS-polyacrylamide gel electrophoresis of the inner membrane immunoprecipitate, which was reduced to a molecular mass of 42 kDa by this enzyme. The 45-kDa protein was readily labeled with [2-3H]mannose, and indeed the radioactivity of the inner membrane immunoprecipitate was almost exclusively present in this component. Moreover, antisera directed against mitochondrial NADH-ubiquinone oxidoreductase (complex I) or F1F0-ATPase (complex V) also precipitated a 45-kDa protein from BRL-3A cell lysates as the predominant mannose-radiolabeled constituent. Endo-β-N-acetylglucosaminidase completely removed the radiolabel from this glycoprotein, and the released oligosaccharides were of the partially trimmed polymannose type (Glc1Man9GlcNAc to Man8GlcNAc). Cycloheximide as well as tunicamycin resulted in total inhibition of radiolabeling of the inner membrane glycoprotein, and moreover, pulse-chase studies employing metrizamide density gradient centrifugation demonstrated that the glycoprotein was initially present in the endoplasmic reticulum (ER) and subsequently appeared in a mitochondrial location. Early movement of the glycoprotein to the mitochondria after synthesis in the ER was also evident from the limited processing undergone by its N-linked oligosaccharides; this stood in contrast to lysosomal glycoproteins in which we noted extensive conversion to complex oligosaccharides. Our findings suggest that the 45-kDa glycoprotein migrates from ER to mitochondria by the previously observed contact sites between the two organelles. Furthermore, the presence of this glycoprotein in at least two major mitochondrial multienzyme complexes would be consistent with a role in mitochondrial translocations.
Quorum Sensing Inhibitors from the Sea Discovered Using Bacterial N-acyl-homoserine Lactone-Based Biosensors

Marine natural products with antibiotic activity have been a rich source of drug discovery; however, the emergence of antibiotic-resistant bacterial strains has turned attention towards the discovery of alternative innovative strategies to combat pathogens. In many pathogenic bacteria, the expression of virulence factors is under the regulation of quorum sensing (QS). QS inhibitors (QSIs) present a promising alternative or potential synergistic treatment since they disrupt the signaling pathway used for intra- and interspecies coordination of expression of virulence factors. This review covers the set of molecules showing QSI activity that were isolated from marine organisms, including plants (algae), animals (sponges, cnidarians, and bryozoans), and microorganisms (bacteria, fungi, and cyanobacteria). The compounds found and the methods used for their isolation are the emphasis of this review.
ER Retention of Soluble Proteins: Retrieval, Retention, or Both?

Pagny et al. ([2000][1]) have recently published an article that touches on a very controversial and important process in the secretory pathway, the export of soluble proteins from the endoplasmic reticulum (ER). The results that are reported confirm data reported previously ([Pedrazzini et al.,
Trk kinase inhibitors as new treatments for cancer and pain

Background: Tropomyosin-related kinases (Trks) are a family of receptor tyrosine kinases activated by neurotrophins. Trks play important roles in pain sensation as well as tumour cell growth and survival signaling. Thus, inhibitors of Trk receptor kinases might provide targeted treatments for pain and cancer. Objective: This paper reviews those patent applications since 2002 claiming small-molecule inhibitors of Trk receptor kinases. Methods: Primary literature and patents were searched with SciFinder and Google Scholar. Patents were selected based on their relevance to Trks and were evaluated and representative compounds were listed as examples. Results/conclusion: Several series of Trk inhibitors with excellent in vitro potencies have been reported and a number of compounds have gone into the clinic. It should be noted that few of these inhibitors are Trk selective, demonstrating that targeting Trk kinases for treatment of pain and/or cancer offers a promising but also challenging approach.
Topical query decomposition

We introduce the problem of query decomposition, where we are given a query and a document retrieval system, and we want to produce a small set of queries whose union of resulting documents corresponds approximately to that of the original query. Ideally, these queries should represent coherent, conceptually well-separated topics. We provide an abstract formulation of the query decomposition problem, and we tackle it from two different perspectives. We first show how the problem can be instantiated as a specific variant of a set cover problem, for which we provide an efficient greedy algorithm. Next, we show how the same problem can be seen as a constrained clustering problem, with a very particular kind of constraint, i.e., clustering with predefined clusters. We develop a two-phase algorithm based on hierarchical agglomerative clustering followed by dynamic programming. Our experiments, conducted on a set of actual queries in a Web scale search engine, confirm the effectiveness of the proposed solutions.
Adenylyl cyclase activity and glucose release from the liver of the European eel, Anguilla anguilla.

The properties of adenylyl cyclase (AC) in liver membranes of the European eel ( Anguilla anguilla) and the involvement of cAMP in glucose release from isolated hepatocytes in response to catecholamines were studied. Basal enzyme activity seemed essentially unaffected by GTP, while a biphasic response to increasing nucleotide concentrations was obtained in the presence of epinephrine. Eel liver AC was dose-dependently stimulated by guanosine 5'- O-(3-thiotriphosphate) and inhibited by guanosine 5'- O-(2-thiodiphosphate). AC activity, intracellular cAMP levels, and glucose release from isolated hepatocytes were significantly enhanced by NaF, forskolin, epinephrine, and phenylephrine. The rise in cAMP production stimulated by catecholamines was counteracted by propranolol, but not by phentolamine. Catecholamine-induced glucose output was instead partially antagonized by both phentolamine and propranolol. Complete inhibition was obtained only by the simultaneous presence of the two adrenergic antagonists. Glucose release from the cells was induced by dibutyryl cAMP and by the calcium ionophore ionomycin. In summary, these data provide the first characterization of eel liver AC system and suggest a direct role for cAMP in the catecholamine-dependent glucose output. Furthermore, the involvement of calcium ions in this cellular response is hypothesized.
CRSS systems for 2012 NIST Speaker Recognition Evaluation

This paper describes the systems developed by the Center for Robust Speech Systems (CRSS), for the 2012 National Institute of Standards and Technology (NIST) Speaker Recognition Evaluation (SRE). Given that the emphasis of SRE'12 is on noisy and short duration test conditions, our system development focused on: (i) novel robust acoustic features, (ii) new feature normalization schemes, (iii) various back-end strategies utilizing multi-session and multi-condition training, and (iv) quality measure based system fusion. Noisy and short duration training/test conditions are artificially generated and effectively utilized. Active speech duration and signal-to-noise-ratio (SNR) estimates are successfully employed as quality measures for system calibration and fusion. Overall system performance was very successful for the given test conditions.
Hospitalization admission control of emergency patients using Markovian Decision Processes and discrete event simulation

This paper addresses the hospitalization admission control policies of patients from an emergency department that should be admitted shortly or transferred. When an emergency patient arrives, depending on his/her health condition, a physician may decide to hospitalize him/her in a specific department. Patient admission depends on the availability of beds, the length of stay (LOS) and the reward of hospitalization which are both patient-class specific. The problem consists in determining patient admission policies in order to maximize the overall gain. We first propose a Markov Decision Process (MDP) Model for determination of the optimal patient admission policy under some restrictive and necessary assumptions such as exponentially distributed LOS. A simulation model is then built to assess MDP admission policies under realistic conditions. We show that MDP policies significantly improve the overall gain for different types of facilities.
Epistatic Effects of Immunoglobulin GM and KM Allotypes on Outcome of Infection with Hepatitis C Virus

ABSTRACT Immunoglobulin GM and KM allotypes—genetic markers of γ and κ chains, respectively—are associated with immune responsiveness to several infectious pathogens and with survival in certain viral epidemics. We hypothesized that GM and KM allotypes affect the outcome of hepatitis C virus (HCV) infection. To test this hypothesis, we serologically allotyped 100 persons with well-documented clearance of HCV infection and 198 matched persistently infected persons. None of the GM or KM phenotypes by itself was associated with the clearance or persistence of HCV infection. Particular combinations of these phenotypes, however, were significantly associated with the outcome of HCV infection. Subjects with GM 1,17 5,13 and KM 1,3 phenotypes were over three times (odds ratio [OR], 3.57; 95% confidence interval [CI], 1.44 to 8.87) as likely to clear the infection as the subjects who lacked these phenotypes. This GM phenotype had a similar association with clearance in the absence of KM 3 (OR, 2.75; 95% CI, 1.21 to 6.23). The presence of GM 1,3,17 23 5,13 phenotype (in the absence of KM 3) was associated with persistence (OR, 0.21; 95% CI, 0.06 to 0.77), while its absence (in the presence of KM 1,3) was associated with the clearance of infection (OR, 2.03; 95% CI, 1.16 to 3.54). These results show epistatic interactions of genes on chromosomes 14 (GM) and 2 (KM) in influencing the outcome of an HCV infection. Further investigations involving candidate genes (GM, KM, HLA, and Fcγ receptors) and cellular and humoral immune responses to HCV epitopes are needed to understand the mechanisms underlying these associations.
Long-Term Hearing Deficits After Childhood Middle Ear Disease

Objectives: To investigate the long-term impact of childhood otitis media on listening ability in school-aged children. Design: Speech perception in background noise was measured in two groups of 35 children, aged 6 to 12 years, with normal middle ear function and sound detection at assessment. The first consisted of children who had previously suffered middle ear disease; the second those with no history of middle ear disease. Results: Binaural speech perception ability was significantly poorer in the children with prior middle ear disease. Furthermore, spatial listening (the ability to selectively attend to a sound signal from one location) was also significantly impaired. Significant correlations were demonstrated between both the age of onset and the duration of childhood otitis media and speech perception ability (onset: r = −0.58, p < 0.001; duration: r = −0.63, p < 0.001). Conclusions: These results demonstrate the risk of long-term functional hearing deficit for children with middle ear disease history in childhood. They also indicate that this risk is increased with earlier onset and longer duration. The findings highlight the need for early intervention and an awareness of the potential for reduced functional listening ability even after sound detection has returned to normal.
Blood Metallothionein Transcript as a Biomarker for Metal Sensitivity: Low Blood Metallothionein Transcripts in Arsenicosis Patients from Guizhou, China

Background Because metallothionein (MT) is a metal-binding protein that protects against metal intoxication, it could be a biomarker for individual sensitivity to metal toxicity. Objective We assessed the use of bloodborne MT transcript as a reflection of tissue MT levels and examined the potential role of MT in arsenic toxicity in an environmentally exposed human population. Method Rodents were treated with zinc or nonmetallic MT inducers for 4 days, and the blood and tissues were collected for MT transcript analysis by real-time reverse transcriptase–polymerase chain reaction and MT protein determination by the cadmium–hemoglobin assay. Blood and buccal cell samples were collected from arsenicosis patients and healthy subjects residing in Guizhou, China, and total RNA was isolated for MT transcript analysis. Results There was a positive correlation between blood MT-1 and MT-2 transcripts and corresponding hepatic or renal MT transcript levels in rats and mice. Furthermore, there was a positive correlation between blood MT-1 and MT-2 transcript and tissue MT protein levels in these animals. A positive correlation also occurred between human blood MT and buccal cell MT transcript levels. MT-1A and MT-2A were the major isoform transcripts in human blood and buccal cells, and significantly lower MT levels were seen in arsenicosis patients compared with healthy subjects. Conclusions Blood MT transcript appears to be a useful biomarker of tissue MT levels. Arsenicosis patients in Guizhou show significantly lower MT transcript levels in blood, which may have predisposed this population to arsenic intoxication.
MicroRNA-183 inhibits gastric cancer proliferation and invasion via directly targeting Bmi-1

The aberrant expression of microRNA-183 (miRNA/miR-183) has been found to be involved in numerous tumor types. However, the role of miR-183 in gastric cancer pathology is unclear and requires investigation. In the present study, the miR-183 expression levels of gastric cancer cell lines and tissues obtained from gastric cancer patients were measured by reverse transcription quantitative polymerase chain reaction analysis. The effect of miR-183 on gastric cancer cell proliferation and invasion was evaluated using MTT, colony formation and Transwell assays. The target of miR-183 was identified and confirmed using a luciferase activity assay. The results revealed that miR-183 was significantly downregulated in gastric cancer cells compared with GES-1 normal gastric epithelial cells. In addition, miR-183 was reduced in gastric cancer tissues compared with adjacent normal tissues. The ectopic expression of miR-183 significantly inhibited gastric cancer cell proliferation, colony formation and invasion. Bmi-1 was also confirmed as a downstream target of miR-183 in the gastric cancer cells by western blot analysis and luciferase activity assays. In conclusion, miR-183 is downregulated in gastric cancer cells and tissues, and inhibits gastric cancer cell proliferation and invasion by targeting Bmi-1. Therefore, targeting miR-183 may be a potential therapeutic strategy in gastric cancer patients.