Miracle-dz/UniFAR-FTUs huggingface dataset:
Susceptibility of p53 Unstructured N Terminus to 20 S Proteasomal Degradation Programs the Stress Response*♦

The N-terminal transcription activation domain of p53 is intrinsically unstructured. We show in vitro and in vivo that this domain initiates p53 degradation by the 20 S proteasome in a ubiquitin-independent fashion. The decay of metabolically labeled p53 follows biphasic kinetics with an immediate fast phase that is ubiquitin-independent and a second slower phase that is ubiquitin-dependent. The 20 S proteasome executes the first phase by default, whereas the second phase requires the 26 S proteasome. p53 N-terminal binding proteins, such as Hdmx, can selectively block the first phase of degradation. Remarkably, γ-irradiation inhibits both p53 decay phases, whereas UV selectively negates the second phase, giving rise to discrete levels of p53 accumulation. Our data of a single protein experiencing double mode degradation mechanisms each with unique kinetics provide the mechanistic basis for programmable protein homeostasis (proteostasis).
Protein Kinase C Mediates Cigarette Smoke/Aldehyde- and Lipopolysaccharide-induced Lung Inflammation and Histone Modifications*

Hongwei Yao, Jae-woong Hwang, Jorge Moscat, Maria T. Diaz-Meco, Michael Leitges, Nandini Kishore, Xiong Li, and Irfan Rahman From the Department of Environmental Medicine, Lung Biology and Disease Program, University of Rochester Medical Center, Rochester, New York 14642, the Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45237, and the Department of Biological Sciences, Pfizer Research Laboratories, St. Louis, Missouri 63167
No stimulation of nitrogen fixation by non‐filamentous diazotrophs under elevated CO2 in the South Pacific

Nitrogen fixation by diazotrophic cyanobacteria is a critical source of new nitrogen to the oligotrophic surface ocean. Research to date indicates that some diazotroph groups may increase nitrogen fixation under elevated pCO2. To test this in natural plankton communities, four manipulation experiments were carried out during two voyages in the South Pacific (30–35oS). High CO2 treatments, produced using 750 ppmv CO2 to adjust pH to 0.2 below ambient, and ‘Greenhouse’ treatments (0.2 below ambient pH and ambient temperature +3 °C), were compared with Controls in trace metal clean deckboard incubations in triplicate. No significant change was observed in nitrogen fixation in either the High CO2 or Greenhouse treatments over 5 day incubations. qPCR measurements and optical microscopy determined that the diazotroph community was dominated by Group A unicellular cyanobacteria (UCYN‐A), which may account for the difference in response of nitrogen fixation under elevated CO2 to that reported previously for Trichodesmium. This may reflect physiological differences, in that the greater cell surface area:volume of UCYN‐A and its lack of metabolic pathways involved in carbon fixation may confer no benefit under elevated CO2. However, multiple environmental controls may also be a factor, with the low dissolved iron concentrations in oligotrophic surface waters limiting the response to elevated CO2. If nitrogen fixation by UCYN‐A is not stimulated by elevated pCO2, then future increases in CO2 and warming may alter the regional distribution and dominance of different diazotroph groups, with implications for dissolved iron availability and new nitrogen supply in oligotrophic regions.
Repression of Sulfate Assimilation Is an Adaptive Response of Yeast to the Oxidative Stress of Zinc Deficiency*

The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. Previous studies identified over 80 genes activated by Zap1 in zinc-limited cells. In this report, we identified 36 genes repressed in a zinc- and Zap1-responsive manner. As a result, we have identified a new mechanism of Zap1-mediated gene repression whereby transcription of the MET3, MET14, and MET16 genes is repressed in zinc-limited cells. These genes encode the first three enzymes of the sulfate assimilation pathway. We found that MET30, encoding a component of the SCFMet30 ubiquitin ligase, is a direct Zap1 target gene. MET30 expression is increased in zinc-limited cells, and this leads to degradation of Met4, a transcription factor responsible for MET3, MET14, and MET16 expression. Thus, Zap1 is responsible for a decrease in sulfate assimilation in zinc-limited cells. We further show that cells that are unable to down-regulate sulfate assimilation under zinc deficiency experience increased oxidative stress. This increased oxidative stress is associated with an increase in the NADP+/NADPH ratio and may result from a decrease in NADPH-dependent antioxidant activities. These studies have led to new insights into how cells adapt to nutrient-limiting growth conditions.
A Structural Determinant That Renders Gαi Sensitive to Activation by GIV/Girdin Is Required to Promote Cell Migration*

Although several non-receptor activators of heterotrimeric G proteins have been identified, the structural features of G proteins that determine their interaction with such activators and the subsequent biological effects are poorly understood. Here we investigated the structural determinants in Gαi3 necessary for its regulation by GIV/girdin, a guanine-nucleotide exchange factor (GEF) that activates Gαi subunits. Using G protein activity and in vitro pulldown assays we demonstrate that Gαi3 is a better substrate for GIV than the highly homologous Gαo. We identified Trp-258 in the Gαi subunit as a novel structural determinant for GIV binding by comparing GIV binding to Gαi3/Gαo chimeras. Mutation of Trp-258 to the corresponding Phe in Gαo decreased GIV binding in vitro and in cultured cells but did not perturb interaction with other Gα-binding partners, i.e. Gβγ, AGS3 (a guanine nucleotide dissociation inhibitor), GAIP/RGS19 (a GTPase-activating protein), and LPAR1 (a G protein-coupled receptor). Activation of Gαi3 by GIV was also dramatically reduced when Trp-258 was replaced with Tyr, Leu, Ser, His, Asp, or Ala, highlighting that Trp is required for maximal activation. Moreover, when mutant Gαi3 W258F was expressed in HeLa cells they failed to undergo cell migration and to enhance Akt signaling after growth factor or G protein-coupled receptor stimulation. Thus activation of Gαi3 by GIV is essential for biological functions associated with Gαi3 activation. In conclusion, we have discovered a novel structural determinant on Gαi that plays a key role in defining the selectivity and efficiency of the GEF activity of GIV on Gαi and that represents an attractive target site for designing small molecules to disrupt the Gαi-GIV interface for therapeutic purposes.
The development of the Amazonian mega-wetland (Miocene; Brazil, Colombia, Peru, Bolivia)

The scenery of Western Amazonia once consisted of fluvial systems that originated on the Amazonian Craton and were directed towards the sub-Andean zone and the Caribbean. In the course of the Early Miocene these fluvial systems were largely replaced by lakes, swamps, tidal channels and marginal marine embayments, forming a mega-wetland. In this chapter we will review the characteristics of this mega-wetland and its different phases of development. These aquatic environments hosted a diverse fauna whereas the shores of these systems were fringed by palm swamps, and a diverse rainforest occurred in the peripheral dry lands. The genesis of this wetland was primarily driven by geological mechanisms such as the Andean uplift, and an increase in accommodation space in the sub-Andean and intracratonic basins. Additionally, high precipitation rates also played an important role in wetland formation. The earliest phase of wetland development is recorded in boreholes drilled in the sub-Andean foreland basins of Peru and Colombia, and in the intracratonic Solimoes Basin of western Brazil. During the latest Oligocene to Early Miocene (~24 to 16 Ma) lacustrine conditions alternated with episodes of Andean and cratonic fluvial drainage as well as marginal marine influence. In Amazonia, marine incursions are intercalated as thin beds in the Middle to Upper Miocene fluvial strata and contain marine and coastal taxa (foraminifera, mangrove pollen). Lacustrine conditions expanded further during the Middle Miocene to early Late Miocene (~16 to 11.3 Ma; Pebas phase). During this period the lake-embayment and swamp systems - fringed by forested lowland - reached their maximum extension. This wetland was subject to marginal marine influence and sustained a large radiation of endemic aquatic invertebrate faunas. During its maximum extent the wetland covered an area of more than 1.5 × 106 km2 - comprising much of the Present western Amazonian lowlands. From the Late Miocene onwards uplift rates in the Eastern Cordillera, Cordillera Real and Cordillera de Merida substantially increased and the Andes became a continuous barrier. This barrier effectively separated lowland Amazonia from Orinoquia and the Magdalena Valley and closed off all lowland connections with the Pacific and the Caribbean. The wetland system became a complex environment where deltaic, estuarine and fluvial environments coexisted. This Late Miocene fluvial-tidal-dominated wetland (~11.3 to 7 Ma, Acre phase) hosted a species-rich vertebrate fauna, but (in contrast to the Pebas phase), the molluscan fauna was species poor and already strongly resembled the modern Amazonian fluvial fauna. This system represents the onset of the transcontinental Amazon River. From 11.3 Ma onwards, sediments of Andean origin reached the Atlantic continental shelf and initiated the build-up of the Amazon Fan.
Corticosteroids and rituximab as adjunctive treatments for thrombotic thrombocytopenic purpura

Although treatment with plasma exchange increased the survival of patients with thrombotic thrombocytopenia purpura to 80% in the 1980s, no further increase of survival occurred over the next 20 years. However, more consistent use of adjuvant treatment with corticosteroids and rituximab in recent years has begun to further increase survival as well as decrease the frequency of relapse. With adjuvant treatment, durable remissions can be achieved more quickly, requiring fewer days of plasma exchange. Fewer days of plasma exchange have resulted in fewer complications, such as central venous catheter‐related systemic infections. Future potential options for adjuvant treatment, recombinant ADAMTS13 to correct severe ADAMTS13 deficiency, and agents to block von Willebrand factor‐mediated platelet thrombosis are being investigated. Am. J. Hematol. 2012. © 2012 Wiley Periodicals, Inc.
Uncovering Knowledge that Supports Malaria Prevention and Control Intervention Program in Ethiopia

Malaria is one of the leading causes of death in Ethiopia. Though there are many efforts to control malaria, the complexity of the problem is still very severe. So there is a need to investigate in detail the synergic effect of risk factors with temperature, altitude, type of visit and malaria type and their causes of death. Hence, in this study an attempt is made to determine the hierarchical importance of different risk factors and their patterns on malaria death occurrence and type of case identification. Knowledge discovery techniques are evaluated to support and uncover knowledge to scale up the malaria prevention and intervention program in Ethiopia. CRISP-DM methodology with classification algorithms such as J48 decision tree, JRip rule induction and Multilayer Perceptron (MLP) Neural Network are adopted to uncover knowledge from total datasets of 37, 609 records. An attempt is made to pre-process the data using business and data understanding with detail statistical summary in order to fill missing values and detect noisy once. Essential target dataset attributes have been constructed by integrating WHO malaria databases, National Metrological data and National Mapping data. Classification techniques discover important attributes/factors that determine malaria cases and occurrence of deaths. J48 Decision tree and MLP correctly classify 95.9% and 97.4%, respectively to predict occurrence of death. The findings of this research indicate that rainfall is the significant factor that determines the prevalence of malaria. When the number of malaria cases increases there is a high probability of death occurrences; the risk is relatively high with those less than 5 years of age. In most zones, malaria transmission rate is high from the month of May to January because of favourable climatic conditions for malaria reproduction.
Locomotor Training and Strength and Balance Exercises for Walking Recovery After Stroke: Response to Number of Training Sessions

Background Evidence-based guidelines are needed to inform rehabilitation practice, including the effect of number of exercise training sessions on recovery of walking ability after stroke. Objective The objective of this study was to determine the response to increasing number of training sessions of 2 interventions-locomotor training and strength and balance exercises-on poststroke walking recovery. Design This is a secondary analysis of the Locomotor Experience Applied Post-Stroke (LEAPS) randomized controlled trial. Setting Six rehabilitation sites in California and Florida and participants' homes were used. Participants Participants were adults who dwelled in the community (N=347), had had a stroke, were able to walk at least 3 m (10 ft) with assistance, and had completed the required number of intervention sessions. Intervention Participants received 36 sessions (3 times per week for 12 weeks), 90 minutes in duration, of locomotor training (gait training on a treadmill with body-weight support and overground training) or strength and balance training. Measurements Talking speed, as measured by the 10-Meter Walk Test, and 6-minute walking distance were assessed before training and following 12, 24, and 36 intervention sessions. Results Participants at 2 and 6 months after stroke gained in gait speed and walking endurance after up to 36 sessions of treatment, but the rate of gain diminished steadily and, on average, was very low during the 25- to 36-session epoch, regardless of treatment type or severity of impairment. Limitations Results may not generalize to people who are unable to initiate a step at 2 months after stroke or people with severe cardiac disease. Conclusions In general, people who dwelled in the community showed improvements in gait speed and walking distance with up to 36 sessions of locomotor training or strength and balance exercises at both 2 and 6 months after stroke. However, gains beyond 24 sessions tended to be very modest. The tracking of individual response trajectories is imperative in planning treatment.
A Human PMS2 Homologue from Aquifex aeolicus Stimulates an ATP-dependent DNA Helicase

Mismatch repair in Escherichia coli involves a number of proteins including MutL and UvrD. Eukaryotes also possess MutL homologues; however, no UvrD helicase homologues have been identified. The hyperthermophilic bacterium Aquifex aeolicus has a MutL protein (Aae MutL) that possesses a latent endonuclease activity similar to eukaryotic, but different from E. coli, MutL proteins. By sequence homology Aq793 is a member of the PcrA/UvrD/Rep helicase subfamily. We expressed Aae MutL and the putative A. aeolicus DNA helicase (Aq793) proteins in E. coli. Using synthetic oligonucleotide substrates, we observed that lower concentrations of Aq793 were required to unwind double-stranded DNA that had a 3′-poly(dT) overhang as compared with double-stranded DNA with a 5′-poly(dT) or lacking a poly(dT) tail. This unwinding activity was stimulated by adding Aae MutL with maximal stimulation observed at an ∼1.5:1 (MutL:Aq793) stoichiometric ratio. The enhancement of Aq793 helicase activity did not require the Aae MutL protein to retain endonuclease activity. Furthermore, the C-terminal 123 amino acid residues of Aae MutL were sufficient to stimulate Aq793 helicase activity, albeit at a significantly reduced efficacy. To the best of our knowledge this is the first time a human PMS2 homologue has been demonstrated to stimulate a PcrA/UvrD/Rep subfamily helicase, and this finding may further our understanding of the evolution of the mismatch repair pathway.
An Integrated Approach for Experimental Target Identification of Hypoxia-induced miR-210*

miR-210 is a key player of cell response to hypoxia, modulating cell survival, VEGF-driven endothelial cell migration, and the ability of endothelial cells to form capillary-like structures. A crucial step in understanding microRNA (miRNA) function is the identification of their targets. However, only few miR-210 targets have been identified to date. Here, we describe an integrated strategy for large-scale identification of new miR-210 targets by combining transcriptomics and proteomics with bioinformatic approaches. To experimentally validate candidate targets, the RNA-induced silencing complex (RISC) loaded with miR-210 was purified by immunoprecipitation along with its mRNA targets. The complex was significantly enriched in mRNAs of 31 candidate targets, such as BDNF, GPD1L, ISCU, NCAM, and the non-coding RNA Xist. A subset of the newly identified targets was further confirmed by 3′-untranslated region (UTR) reporter assays, and hypoxia induced down-modulation of their expression was rescued blocking miR-210, providing support for the approach validity. In the case of 9 targets, such as PTPN1 and P4HB, miR-210 seed-pairing sequences localized in the coding sequence or in the 5′-UTR, in line with recent data extending miRNA targeting beyond the “classic” 3′-UTR recognition. Finally, Gene Ontology analysis of the targets highlights known miR-210 impact on cell cycle regulation and differentiation, and predicts a new role of this miRNA in RNA processing, DNA binding, development, membrane trafficking, and amino acid catabolism. Given the complexity of miRNA actions, we view such a multiprong approach as useful to adequately describe the multiple pathways regulated by miR-210 during physiopathological processes.
Cost and effectiveness of treatments for mild‐to‐moderate bleeding episodes in haemophilia patients with inhibitors in Korea

Summary. First‐line treatment for mild‐to‐moderate bleeding episodes in patients with haemophilia and inhibitors in Korea is currently activated prothrombin complex concentrate (aPCC) with recombinant activated factor VII (rFVIIa) as second‐line therapy or as a last resort. The aim of this study was to estimate the cost and effectiveness of aPCC vs. rFVIIa for treating mild‐to‐moderate bleeds in inhibitor patients from the Korean reimbursement authorities’ perspective. Clinical outcomes and resource utilization data (number of doses, average dose, number of outpatient visits, inpatient stays, ambulance transport and concomitant medications) were collected from an observational study involving four Korean paediatric haemophilia centres. Cost‐effectiveness was modelled using a decision analysis approach and sensitivity analyses undertaken. rFVIIa was a more effective haemostatic therapy (87.1% efficacy in bleed resolution) than aPCC (64.0%). rFVIIa effected more rapid haemostasis, resolving bleeding in a mean of 6.6 h vs. 25.2 h for aPCC. Fewer rFVIIa doses were required per bleed vs. aPCC (means 1.7 and 2.3). Mean total direct medical costs from bleed initiation to cessation were estimated at Korean Won (KRW)12 460 thousand (US$12 311) for rFVIIa given as first‐line therapy and KRW18 304 thousand (US$18 085) for aPCC given as first‐line therapy. Sensitivity analyses confirmed the cost‐effectiveness of rFVIIa vs. aPCC given as first‐line therapy. In Korea, use of rFVIIa as first‐line therapy for treatment of mild‐to‐moderate bleeding episodes in inhibitor patients is both clinically effective and cost‐effective compared with initial aPCC treatment. rFVIIa should be considered as the first‐line treatment for mild‐to‐moderate bleeding episodes in patients with haemophilia and inhibitors in Korea.
Arthroscopic subacromial decompression: one- to seven-year results

Objectives: Impingement syndrome is one of the most important causes of pain in the shoulder region. Advances in arthroscopic techniques allowed acromioplasty to be performed arthroscopically. In this study, we evaluated the results of arthroscopic subacromial decompression in patients with impingement syndrome. Methods: Seventy patients who were treated with arthroscopic subacromial decompression and who had a follow-up period of at least a year were retrospectively evaluated. There were 51 females and 19 males (mean age 41.2 years, range 20 to 72 years). Additional surgical procedures involved debridement in massive rotator cuff tears (n=2), biceps tenodesis (n=7), distal clavicle resection (n=7), and posterior capsular release (n=8). Evaluations were made using physical examination and radiography findings, and the Constant scoring system. The mean follow-up period was 27.6 months (range 12 to 84 months). Results: In none of the patients failure was encountered. Sixty patients (85%) achieved excellent and good results. The results were satisfactory in 10 patients (15%). One patient developed postoperative frozen shoulder which was unresponsive to physical therapy and was treated with arthroscopic capsular release. Conclusion: Arthroscopic subacromial decompression is a superior surgical method for appropriately selected patients in the hands of experienced shoulder arthroscopists. Patients undergoing arthroscopic subacromial decompression can return to their daily and athletic activities very early because of relatively small surgical injuries and the preservation of the deltoid attachment.
Mechanism of Action of an Imidopiperidine Inhibitor of Human Polynucleotide Kinase/Phosphatase*

The small molecule, 2-(1-hydroxyundecyl)-1-(4-nitrophenylamino)-6-phenyl-6,7a-dihydro-1H-pyrrolo[3,4-b]pyridine-5,7(2H,4aH)-dione (A12B4C3), is a potent inhibitor of the phosphatase activity of human polynucleotide kinase/phosphatase (PNKP) in vitro. Kinetic analysis revealed that A12B4C3 acts as a noncompetitive inhibitor, and this was confirmed by fluorescence quenching, which showed that the inhibitor can form a ternary complex with PNKP and a DNA substrate, i.e. A12B4C3 does not prevent DNA from binding to the phosphatase DNA binding site. Conformational analysis using circular dichroism, UV difference spectroscopy, and fluorescence resonance energy transfer all indicate that A12B4C3 disrupts the secondary structure of PNKP. Investigation of the potential site of binding of A12B4C3 to PNKP using site-directed mutagenesis pointed to interaction between Trp402 of PNKP and the inhibitor. Cellular studies revealed that A12B4C3 sensitizes A549 human lung cancer cells to the topoisomerase I poison, camptothecin, but not the topoisomerase II poison, etoposide, in a manner similar to small interfering RNA against PNKP. A12B4C3 also inhibits the repair of DNA single and double strand breaks following exposure of cells to ionizing radiation, but does not inhibit two other key strand-break repair enzymes, DNA polymerase β or DNA ligase III, providing additional evidence that PNKP is the cellular target of the inhibitor.