Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal assessment of associations between food insecurity, antiretroviral adherence and HIV treatment outcomes in rural Uganda

Introduction:Food insecurity is a potentially important barrier to the success of antiretroviral therapy (ART) programs in resource-limited settings. We undertook a longitudinal study in rural Uganda to estimate the associations between food insecurity and HIV treatment outcomes. Design:Longitudinal cohort study. Methods:Participants were from the Uganda AIDS Rural Treatment Outcomes study and were followed quarterly for blood draws and structured interviews. We measured food insecurity with the validated Household Food Insecurity Access Scale. Our primary outcomes were: ART nonadherence (adherence <90%) measured by visual analog scale; incomplete viral load suppression (>400 copies/ml); and low CD4+ T-cell count (<350 cells/&mgr;l). We used generalized estimating equations to estimate the associations, adjusting for socio-demographic and clinical variables. Results:We followed 438 participants for a median of 33 months; 78.5% were food insecure at baseline. In adjusted analyses, food insecurity was associated with higher odds of ART nonadherence [adjusted odds ratio (AOR) 1.56, 95% confidence interval (CI) 1.10–2.20, P < 0.05], incomplete viral suppression (AOR 1.52, 95% CI 1.18–1.96, P < 0.01), and CD4+ T-cell count less than 350 (AOR 1.47, 95% CI 1.24–1.74, P < 0.01). Adding adherence as a covariate to the latter two models removed the association between food insecurity and viral suppression, but not between food insecurity and CD4+ T-cell count. Conclusions:Food insecurity is longitudinally associated with poor HIV outcomes in rural Uganda. Intervention research is needed to determine the extent to which improved food security is causally related to improved HIV outcomes and to identify the most effective policies and programs to improve food security and health.
Identification of Outer Membrane Proteins from an Antarctic Bacterium Pseudomonas syringae Lz4W*

Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.
The RNA-Binding Protein Rrm4 is Essential for Efficient Secretion of Endochitinase Cts1

Long-distance transport of mRNAs is crucial in determining spatio-temporal gene expression in eukaryotes. The RNA-binding protein Rrm4 constitutes a key component of microtubule-dependent mRNA transport in filaments of Ustilago maydis. Although a number of potential target mRNAs could be identified, cellular processes that depend on Rrm4-mediated transport remain largely unknown. Here, we used differential proteomics to show that ribosomal, mitochondrial, and cell wall-remodeling proteins, including the bacterial-type endochitinase Cts1, are differentially regulated in rrm4Δ filaments. In vivo UV crosslinking and immunoprecipitation and fluorescence in situ hybridization revealed that cts1 mRNA represents a direct target of Rrm4. Filaments of cts1Δ mutants aggregate in liquid culture suggesting an altered cell surface. In wild type cells Cts1 localizes predominantly at the growth cone, whereas it accumulates at both poles in rrm4Δ filaments. The endochitinase is secreted and associates most likely with the cell wall of filaments. Secretion is drastically impaired in filaments lacking Rrm4 or conventional kinesin Kin1 as well as in filaments with disrupted microtubules. Thus, Rrm4-mediated mRNA transport appears to be essential for efficient export of active Cts1, uncovering a novel molecular link between mRNA transport and the mechanism of secretion.
Targeted Proteomics of the Eicosanoid Biosynthetic Pathway Completes an Integrated Genomics-Proteomics-Metabolomics Picture of Cellular Metabolism*

Eicosanoids constitute a diverse class of bioactive lipid mediators that are produced from arachidonic acid and play critical roles in cell signaling and inflammatory aspects of numerous diseases. We have previously quantified eicosanoid metabolite production in RAW264.7 macrophage cells in response to Toll-like receptor 4 signaling and analyzed the levels of transcripts coding for the enzymes involved in the eicosanoid metabolite biosynthetic pathways. We now report the quantification of changes in protein levels under similar experimental conditions in RAW264.7 macrophages by multiple reaction monitoring mass spectrometry, an accurate targeted protein quantification method. The data complete the first fully integrated genomic, proteomic, and metabolomic analysis of the eicosanoid biochemical pathway.
Prescription of Cancer Treatment Modalities in Developing Countries: Results from a Multi-Centre Observational Study

Background: Treatment is an important component of a comprehensive cancer control approach and its outcomes strongly depend on infrastructure, equipment, human and financial resources available. Therefore it is imperative to generate evidence-based tools to assist health policy mak- ers from low resourced countries in planning efficient and equitable treatment services for a de- fined population based on what it is feasible to these settings. Methods: The intended cancer spe- cific treatment planned and written in the patients' medical record (treatment prescription) of untreated adult cancer cases (≥18 years of age), excluding non-melanoma skin cancer, was re- corded in a chronological way from 1 January 2012 onwards in a group of eight comprehensive cancer centres located in middle income countries and offering the main modalities of cancer
Zerebrale perfusions-CT : Theoretische grundlagen, methodische realisierung und praktische erfahrungen in der diagnostik des ischämischen hirninfarktes

Cerebral perfusion CT using dynamic CT after bolus injection of contrast has recently been introduced in the clinical management of stroke patients. Based on the indicator dilution principle various theoretical models can be formulated which all aim at the quantitative determination of cerebral blood flow (CBF). Our Perfusion CT approach is based on the maximum slope model and allows in addition to the calculation of CBF parameter images the display of cerebral blood volume (CBV) and time to peak as diagnostically meaningful parameters. This approach allows the detection of acute ischemia of the supratentorial brain with a sensitivity of 91 % and has proven its value as a routine diagnostic tool for acute stroke. The combination of various functional maps provides excellent information regarding the type of ischemia. Although the direct assessment of ischemia using absolute CBF values is severely restricted by patient dependent systematic errors, the severity of ischemia may reliably be assessed by using relative CBF perfusion indices.
NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.

SUMMARY In plants, both transcriptional (TGS) and post-transcriptional gene silencing (PTGS) can be self-reinforcing, and this allows maintenance of silencing once the initiator has been removed or suppressed. For TGS, this can be accomplished by the generation of small interfering RNAs (siRNAs) from methylated DNA templates by RNA polymerase IV (PolIV), RNA-dependent RNA polymerase 2 (RDR2), DICER-LIKE 3 (DCL3), and the RNA-directed DNA methylation (RdDM) machinery. Maintenance of PTGS requires RNA-dependent RNA polymerase 6 (RDR6), and may be associated with DNA methylation and transitive production of secondary siRNAs. In this work, mutants defective for the NRPD1a and NRPD1b alternative largest subunits of PolIV were tested for their ability to undergo RdDM, transitive RNA silencing and maintenance of PTGS. PTGS could be initiated in both nrpd1a and nrpd1b mutants, and this was associated with production of secondary siRNAs; silencing was not maintained however. nrpd1a mutants could support RdDM although this was lost upon reversal of silencing, as was methylation in rdr6 mutants. We conclude that components of the machinery that maintain TGS are required for maintenance of PTGS, and that RDR6 uses distinct templates in the initiation and maintenance phases of RNA silencing.
Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism, and highlights the importance of mitochondrial metabolism.

SUMMARY The application of nitrogen to legumes regulates seed metabolism and composition. We recently showed that the seed-specific overexpression of amino acid permease VfAAP1 increases amino acid supply, and the levels of N and protein in the seeds. Two consecutive field trials using Pisum sativum AAP1 lines confirmed increases in the levels of N and globulin in seed; however, compensatory changes of sucrose/starch and individual seed weight were also observed. We present a comprehensive analysis of AAP1 seeds using combinatorial transcript and metabolite profiling to monitor the effects of nitrogen supply on seed metabolism. AAP1 seeds have increased amino acids and stimulated gene expression associated with storage protein synthesis, maturation, deposition and vesicle trafficking. Transcript/metabolite changes reveal the channelling of surplus N into the transient storage pools asparagine and arginine, indicating that asparagine synthase is transcriptionally activated by high N levels and/or C limitation. Increased C-acceptor demand for amino acid synthesis, resulting from elevated levels of N in seeds, initiates sucrose mobilization and sucrose-dependent pathways via sucrose synthase, glycolysis and the TCA cycle. The AAP1 seeds display a limitation in C, which leads to the catabolism of arginine, glutamic acid and methionine to putrescine, beta-alanine and succinate. Mitochondria are involved in the coordination of C/N metabolism, with branched-chain amino acid catabolism and a gamma-amino-butyric acid shunt. AAP1 seeds contain higher levels of ABA, which is possibly involved in storage-associated gene expression and the N-dependent stimulation of sucrose mobilization, indicating that a signalling network of C, N and ABA is operating during seed maturation. These results demonstrate that legume seeds have a high capacity to regulate N:C ratios, and highlight the importance of mitochondria in the control of N-C balance and amino acid homeostasis.
Five Friends of Methylated Chromatin Target of Protein-Arginine-Methyltransferase[Prmt]-1 (Chtop), a Complex Linking Arginine Methylation to Desumoylation*

Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop (5FMC). 5FMC is a nuclear complex that can only be recruited by Chtop when the latter is arginine-methylated by Prmt1. It consists of the co-activator Pelp1, the Sumo-specific protease Senp3, Wdr18, Tex10, and Las1L. Pelp1 functions as the core of 5FMC, as the other components become unstable in the absence of Pelp1. We show that recruitment of 5FMC to Zbp-89, a zinc-finger transcription factor, affects its sumoylation status and transactivation potential. Collectively, our data provide a mechanistic link between arginine methylation and (de)sumoylation in the control of transcriptional activity.
Advances in Wound Photography and Assessment Methods

PURPOSE To provide the wound care practitioner with an overview of new methodologies for measuring and documenting chronic wounds. TARGET AUDIENCE This continuing education activity is intended for physicians and nurses with an interest in wound care and related disorders. OBJECTIVES After reading this article and taking this test, the reader should be able to: Recognize the importance of thorough wound assessment. Describe the new aspects of chronic wound assessment. Identify the technologies and methods to measure and document wounds.
Functional Proteomic Analysis of Long-term Growth Factor Stimulation and Receptor Tyrosine Kinase Coactivation in Swiss 3T3 Fibroblasts*

In Swiss 3T3 fibroblasts, long-term stimulation with PDGF, but not insulin-like growth factor 1 (IGF-1) or EGF, results in the establishment of an elongated migratory phenotype, characterized by the formation of retractile dendritic protrusions and absence of actin stress fibers and focal adhesion complexes. To identify receptor tyrosine kinase-specific reorganization of the Swiss 3T3 proteome during phenotypic differentiation, we compared changes in the pattern of protein synthesis and phosphorylation during long-term exposure to PDGF, IGF-1, EGF, and their combinations using 2DE-based proteomics after 35S- and 33P-metabolic labeling. One hundred and five differentially regulated proteins were identified by mass spectrometry and some of these extensively validated. PDGF stimulation produced the highest overall rate of protein synthesis at any given time and induced the most sustained phospho-signaling. Simultaneous activation with two or three of the growth factors revealed both synergistic and antagonistic effects on protein synthesis and expression levels with PDGF showing dominance over both IGF-1 and EGF in generating distinct proteome compositions. Using signaling pathway inhibitors, PI3K was identified as an early site for signal diversification, with sustained activity of the PI3K/AKT pathway critical for regulating late protein synthesis and phosphorylation of target proteins and required for maintaining the PDGF-dependent motile phenotype. Several proteins were identified with novel PI3K/Akt-dependent synthesis and phosphorylations including eEF2, PRS7, RACK-1, acidic calponin, NAP1L1, Hsp73, and fascin. The data also reveal induction/suppression of key F-actin and actomyosin regulators and chaperonins that enable PDGFR to direct the assembly of a motile cytoskeleton, despite simultaneous antagonistic signaling activities. Together, the study demonstrates that long-term exposure to different growth factors results in receptor tyrosine kinase-specific regulation of relatively small subproteomes, and implies that the strength and longevity of receptor tyrosine kinase-specific signals are critical in defining the composition and functional activity of the resulting proteome.
A hierarchical tin/carbon composite as an anode for lithium-ion batteries with a long cycle life.

Tin is a promising anode candidate for next-generation lithium-ion batteries with a high energy density, but suffers from the huge volume change (ca. 260 %) upon lithiation. To address this issue, here we report a new hierarchical tin/carbon composite in which some of the nanosized Sn particles are anchored on the tips of carbon nanotubes (CNTs) that are rooted on the exterior surfaces of micro-sized hollow carbon cubes while other Sn nanoparticles are encapsulated in hollow carbon cubes. Such a hierarchical structure possesses a robust framework with rich voids, which allows Sn to alleviate its mechanical strain without forming cracks and pulverization upon lithiation/de-lithiation. As a result, the Sn/C composite exhibits an excellent cyclic performance, namely, retaining a capacity of 537 mAh g(-1) for around 1000 cycles without obvious decay at a high current density of 3000 mA g(-1) .
Identification and Selected Reaction Monitoring (SRM) Quantification of Endocytosis Factors Associated with Numb*

Numb is an endocytic adaptor protein that regulates the endocytosis and trafficking of transmembrane receptors including Notch, E-cadherin, and integrins. Vertebrate Numb is alternatively spliced at exons 3 and 9 to give rise to four protein isoforms. Expression of these isoforms varies at different developmental stages, and although the function of Numb isoforms containing exon 3 has been studied, the role of exon 9 inclusion has not been shown. Here we use affinity purification and tandem mass spectrometry to identify Numb associated proteins, including novel interactions with REPS1, BMP2K, and BCR. In vitro binding measurements indicated exon 9-independent Numb interaction with REPS1 and Eps15 EH domains. Selected reaction monitoring mass spectrometry was used to quantitatively compare the proteins associated with the p72 and p66 Numb isoforms, which differ by the exon 9 region. This showed that significantly more EPS15 and three AP-2 subunit proteins bound Numb isoforms containing exon 9. The EPS15 preference for exon 9-containing Numb was confirmed in intact cells by using a proximity ligation assay. Finally, we used multiplexed selected reaction monitoring mass spectrometry to assess the dynamic regulation of Numb association with endocytic proteins. Numb hyper-phosphorylation resulted in disassociation of Numb endocytic complexes, while inhibition of endocytosis did not alter Numb association with the AP-2 complex but altered recruitment of EPS15, REPS1, and BMP2K. Hence, quantitative mass spectrometric analysis of Numb protein-protein interactions has provided new insights into the assembly and regulation of protein complexes important in development and cancer.
Squeezers and Leaf-cutters: Differential Diversification and Degeneration of the Venom System in Toxicoferan Reptiles*

Although it has been established that all toxicoferan squamates share a common venomous ancestor, it has remained unclear whether the maxillary and mandibular venom glands are evolving on separate gene expression trajectories or if they remain under shared genetic control. We show that identical transcripts are simultaneously expressed not only in the mandibular and maxillary glands, but also in the enigmatic snake rictal gland. Toxin molecular frameworks recovered in this study were three-finger toxin (3FTx), CRiSP, crotamine (beta-defensin), cobra venom factor, cystatin, epididymal secretory protein, kunitz, l-amino acid oxidase, lectin, renin aspartate protease, veficolin, and vespryn. We also discovered a novel low-molecular weight disulfide bridged peptide class in pythonid snake glands. In the iguanian lizards, the most highly expressed are potentially antimicrobial in nature (crotamine (beta-defensin) and cystatin), with crotamine (beta-defensin) also the most diverse. However, a number of proteins characterized from anguimorph lizards and caenophidian snakes with hemotoxic or neurotoxic activities were recruited in the common toxicoferan ancestor and remain expressed, albeit in low levels, even in the iguanian lizards. In contrast, the henophidian snakes express 3FTx and lectin toxins as the dominant transcripts. Even in the constricting pythonid and boid snakes, where the glands are predominantly mucous-secreting, low-levels of toxin transcripts can be detected. Venom thus appears to play little role in feeding behavior of most iguanian lizards or the powerful constricting snakes, and the low levels of expression argue against a defensive role. However, clearly the incipient or secondarily atrophied venom systems of these taxa may be a source of novel compounds useful in drug design and discovery.
The Nuclear Protein ALY Binds to and Modulates the Activity of Transcription Factor E2F2*

E2F transcription factors control the expression of genes involved in a variety of essential cellular processes and consequently their activity needs to be tightly regulated. Protein-protein interactions are thought to be key modulators of E2F activity. To gain insight into the mechanisms that regulate the activity of E2F2, we searched for novel proteins that associate with this transcription factor. We show that the nuclear protein ALY (THO complex 4), originally described as a transcriptional co-activator, associates with DNA-bound E2F2 and represses its transcriptional activity. The capacity of ALY to modulate gene expression was analyzed with expression microarrays by characterizing the transcriptome of E2F2 expressing HEK293T cells in which ALY was either overexpressed or silenced. We show that ALY influences the expression of more than 400 genes, including 98 genes bearing consensus E2F motifs. Thus, ALY emerges as a novel E2F2-interacting protein and a relevant modulator of E2F-responsive gene expression.
One-pot synthesis of CdS nanocrystals hybridized with single-layer transition-metal dichalcogenide nanosheets for efficient photocatalytic hydrogen evolution.

Exploration of low-cost and earth-abundant photocatalysts for highly efficient solar photocatalytic water splitting is of great importance. Although transition-metal dichalcogenides (TMDs) showed outstanding performance as co-catalysts for the hydrogen evolution reaction (HER), designing TMD-hybridized photocatalysts with abundant active sites for the HER still remains challenge. Here, a facile one-pot wet-chemical method is developed to prepare MS2-CdS (M=W or Mo) nanohybrids. Surprisedly, in the obtained nanohybrids, single-layer MS2 nanosheets with lateral size of 4-10 nm selectively grow on the Cd-rich (0001) surface of wurtzite CdS nanocrystals. These MS2-CdS nanohybrids possess a large number of edge sites in the MS2 layers, which are active sites for the HER. The photocatalytic performances of WS2-CdS and MoS2-CdS nanohybrids towards the HER under visible light irradiation (>420 nm) are about 16 and 12 times that of pure CdS, respectively. Importantly, the MS2-CdS nanohybrids showed enhanced stability after a long-time test (16 h), and 70% of catalytic activity still remained.