Miracle-dz/UniFAR-FTUs huggingface dataset:
Disturbance macroecology: a comparative study of community structure metrics in a high‐severity disturbance regime

Author(s): Newman, Erica A; Wilber, Mark Q; Kopper, Karen E; Moritz, Max A; Falk, Donald A; McKenzie, Don; Harte, John | Abstract: Macroecological studies have established widespread patterns of species diversity and abundance in ecosystems but have generally restricted their scope to relatively steady‐state systems. As a result, how macroecological metrics are expected to scale in ecosystems that experience natural disturbance regimes is unknown. We examine macroecological patterns in a fire‐dependent forest of Bishop pine (Pinus muricata ). We target two different‐aged stands in a stand‐replacing fire regime: a mature stand with a diverse understory and with no history of major disturbance for at least 40 yr, and one disturbed by a stand‐replacing fire 17 yr prior to measurement. We compare properties of these stands with macroecological predictions from the Maximum Entropy Theory of Ecology (METE ), an information entropy‐based theory that has proven highly successful in predicting macroecological metrics in multiple ecosystems and taxa. Ecological patterns in the mature stand more closely match METE predictions than do data from the more recently disturbed, mid‐seral stage stand. This suggests METE 's predictions are more robust in late‐successional, slowly changing, or steady‐state systems than those in rapid flux with respect to species composition, abundances, and organisms’ sizes. Our findings highlight the need for a macroecological theory that incorporates natural disturbance, perturbations, and ecological dynamics into its predictive capabilities, because most natural systems are not in a steady state.
ERCC1-XPF Interacts with Topoisomerase IIβ to Facilitate the Repair of Activity-induced DNA Breaks

Type II DNA Topoisomerases (TOP II) generate transient double-strand DNA breaks (DSBs) to resolve topological constraints during transcription. Using genome-wide mapping of DSBs and functional genomics approaches, we show that, in the absence of exogenous genotoxic stress, transcription leads to DSB accumulation and to the recruitment of the structure-specific ERCC1-XPF endonuclease on active gene promoters. Instead, we find that the complex is released from regulatory or gene body elements in UV-irradiated cells. Abrogation of ERCC1 or re-ligation blockage of TOP II-mediated DSBs aggravates the accumulation of transcription-associated γH2Ax and 53BP1 foci, which dissolve when TOP II-mediated DNA cleavage is inhibited. An in vivo biotinylation tagging strategy coupled to a high-throughput proteomics approach reveals that ERCC1-XPF interacts with TOP IIβ and the CTCF/cohesin complex, which co-localize with the heterodimer on DSBs. Together; our findings provide a rational explanation for the remarkable clinical heterogeneity seen in human disorders with ERCC1-XPF defects.
A Novel Two-Level Optimization Strategy for Multi-Debris Active Removal Mission in LEO

: Recent studies of the space debris environment in Low Earth Orbit (LEO) have shown that the critical density of space debris has been reached in certain regions. The Active Debris Removal (ADR) mission, to mitigate the space debris density and stabilize the space debris environment, has been considered as a most effective method. In this paper, a novel two-level optimization strategy for multi-debris removal mission in LEO is proposed, which includes the low-level and high-level optimization process. To improve the overall performance of the multi-debris active removal mission and obtain multiple Pareto-optimal solutions, the ADR mission is seen as a Time-Dependant Traveling Salesman Problem (TDTSP) with two objective functions to minimize the total mission duration and the total propellant consumption. The problem includes the sequence optimization to determine the sequence of removal of space debris and the transferring optimization to define the orbital maneuvers. Two optimization models for the two-level optimization strategy are built in solving the multi-debris removal mission, and the optimal Pareto solution is successfully obtained by using the non-dominated sorting genetic algorithm II (NSGA-II). Two test cases are presented, which show that the low level optimization strategy can successfully obtain the optimal sequences and the initial solution of the ADR mission and the high level optimization strategy can efficiently and robustly find the feasible optimal solution for long duration perturbed rendezvous problem.
Readability of Narrative Disclosures, and Corporate Liquidity and Payout Policies

Abstract In this paper, we examine the relation between the readability of narrative disclosures in 10-K reports, and corporate liquidity and payout policies. We find that firms with less readable disclosures hold significantly more cash. We also find that this relationship is stronger for firms with weak corporate governance, and with higher financing constraints and refinancing risks. Further analysis also shows that firms with less readable disclosures pay fewer cash dividends and repurchase less stock. Our findings are robust to different estimation methods, and to alternative specifications of key variables. The findings from this study contribute to the emerging research that stresses the importance of 10-K report readability in protecting shareholder wealth.
TRITON2: An international, multicenter, open-label, phase II study of the PARP inhibitor rucaparib in patients with metastatic castration-resistant prostate cancer (mCRPC) associated with homologous recombination deficiency (HRD).

TPS388Background: Up to 25% of patients with advanced prostate cancer, including mCRPC, have a deleterious germline or somatic mutation in BRCA1, BRCA2, ATM or another homologous recombination (HR) DNA repair gene that can serve as a molecular marker to select those who may respond to poly(ADP-ribose) polymerase inhibitors (PARPis). PARPis are lethal to cells with HRD, and PARPi treatment has shown preliminary evidence of an antitumor effect in patients with mCRPC who harbor a mutation in an HR DNA repair gene (Mateo et al. N Engl J Med. 2015;373:1697-708). These data provide a compelling rationale for evaluating rucaparib, a potent PARP1, PARP2 and PARP3 inhibitor, in patients with mCRPC associated with HRD. Methods: TRITON2 (NCT02952534) is a phase 2 study evaluating rucaparib 600 mg BID in patients with mCRPC. Patients with a deleterious germline or somatic BRCA1, BRCA2 or ATM mutation (per prior local test or central test during screening) will be enrolled into 1 of 2 cohorts based on the presence or .
Comparison occlusion between closed and open reduction of unilateral condylar fractures: a randomized controlled trial

Objective To compare occlusion, outcome and complications with the closed method versus theopen method of treatment for unilateral mandibular condylar fracture.Methods Twenty patients with unilateral mandibular condylar fractures (neck or subcondyle) ofthe mandible were evaluated. The patients were randomly divided into two groups, with group 1receiving closed reduction and group 2 receiving open reduction and internal fi xation. Patients werefollowed up for a period of 3 months.Results No statistically signi fi cant differences between the open and closed treatment methodswere found in terms of occlusion, interincisive distance, temporomandibular joint (TMJ) pain, TMJclicking and period of hospital stay. Statistically signi fi cant improvement was seen in group 2 compared with group 1 in terms of chin deviation on mouth opening. Group 1 had shorter operationtimes and less postoperative pain scores than group 2. None of the Group 2 patients developedpermanent facial nerve damage or unsightly scarring.Conclusions There is no statistically signi fi cant difference between the two methods in termsof occlusion. A statistically signi fi cant difference was seen in the patients treated with the openmethod, with improved chin swaying compared with those treated with the closed method.
The use of optical coherence tomography as a diagnostic tool for dental caries

Dental caries is one of the most common human diseases, 60-90% of school children world-wide have dental cavities. Severity can vary, from early demineralisation, which preventive measures can improve, to cavitation, leading to fillings. Different diagnostic tools are available, such as clinical examination, radiographic investigation and Enhanced Visual examination/In-ternational Caries Detection and Assessment System (ICDAS). To date, there is no universal diagnostic tool that can be used to detect carious lesions at the very early stages. Optical Coherence Tomography (OCT) is a non-invasive and ionising radiation free technique that has been used in dentistry, but not to diagnose caries. // The aim of this research was to investigate the use of OCT imaging in dentistry as a routine, and adjunct clinical diagnostic tool for dental caries, by developing standardised markers for each ICDAS score, and to compare the results with conventional clinical methods i.e. radio-graphs and ICDAS. In addition, markers in the OCT scan and scattering profile intensity plots for both sound and carious affected teeth were determined, to aid diagnosis. // All specimens were collected from patients undergoing dental treatment at Eastman Dental Hospital. Extracted human primary and permanent teeth (N>180) with varying caries severity were collected under ethical approval, after obtaining informed consent according to the inclu-sion and exclusion criteria. Photographic and radiographic images of tooth samples were taken and categorised according to the ICDAS system. Samples were then imaged using OCT (VivoSight OCT Scanner) with each lesion scanned separately (N>200). The scattering inten-sity profiles were plotted. In healthy samples, OCT B-scans showed a homogenous pattern of scattering intensity throughout enamel structure indicating healthy structure while in carious teeth, a non-homogenous scattering intensity was observed indicating changes in enamel structure. // Different scattering intensity profiles for each ICDAS score were observed, and empirical markers were developed for each score. This led to establishing scattering fingerprints for each type of ICDAS lesion. A multi-assessor’s analysis, followed by a kappa analysis, was carried to evaluate the selectivity and accuracy of the makers. The results showed moderate to substantial strength of agreement in both intra-rater and inter-rater reliability. // In conclusion, OCT has been shown to be a safe, useful, reliable and non-destructive tech-nique that can investigate the internal structure by measuring the back-scattered light from enamel and dentine. OCT provides an understanding of the lesion in terms of depth and ex-tent, therefore helping in predicting the lesion’s prognosis, which is not found in conventional methods. In addition, OCT helps to differentiate between carious and sound teeth, and addi-tionally between different ICDAS scores. The definition of specific scattering markers for each type of caries lesions will enable us to bring this technique one-step closer to the clinic.
Particle Swarm Optimization: A Powerful Technique for Solving Engineering Problems

This chapter will introduce the particle swarm optimization (PSO) algorithm giving an overview of it. In order to formally present the mathematical formulation of PSO algorithm, the classical version will be used, that is, the inertial version; meanwhile, PSO variants will be summarized. Besides that, hybrid methods representing a combination of heuristic and deterministic optimization methods are going to be presented as well. Before the presentation of these algorithms, the reader will be introduced to the main challenges when approaching PSO algorithm. Two study cases of diverse nature, one regarding the PSO in its classical version and another one regarding the hybrid version, are provided in this chapter showing how handful and versatile it is to work with PSO. The former case is the optimization of a mechanical structure in the nuclear fuel bundle and the last case is the optimization of the cost function of a cogeneration system using PSO in a hybrid optimization. Finally, a conclusion is presented.
Smallholder Farmers Vulnerability Level to Climate Change Impacts and Implications to Agricultural Production in Tigray Regional State, Northern Ethiopia

Vulnerability to climate change impact is the most pressing issues for less developed countries whose economy mainly depends on the agricultural sector. The demand for food is growing swiftly whereas impacts of climate change on the global food production are increasing. More area specific research outputs and evidences-based policy directions are needed to tackle the ever changing climate and to reduce its impacts on the agricultural production. The aim of this study was to investigate subsistence farmer household’s vulnerability level to climate change impacts and its associations with household’s agricultural production. Then primary data was collected from 400 households from Kolla Temben District, Tigray Regional State, North Ethiopia. Multistage sampling techniques were applied to select households for interview from the district. In the first stage, 4 Kebelles (Kebelle - administration unit) were selected randomly out of 27 Kebelles and then400 households were selected for interview through systematic random sampling techniques (Figure 1). Multiple regressions were used to examine the associations between household’s vulnerability to climate change impacts and agricultural production. Grounded theory and content analysis techniques were use to analyze data from key informant interviews and focus group discussions. For every single unit increase in household vulnerability to climate change impacts, there was an average agricultural production decrease between 16.99 and 25.83 (Table 4). For single unit increase in household’s vulnerability to climate change impact, there was a decrease of total crop production, Total income, total livestock, total food consumption and food consumption per adult equivalent. Rainfall decrease, small farmland ownership, steep topography, frequent flood occurrences and large family size are among the major factors that negatively affect household’s agricultural production and total income. The more the vulnerable the households, the less in total annual crop production, total livestock size, total income from agricultural production and the more dependent on food aid). There is a negative association between household’s vulnerability level to climate change impacts and agricultural production (crop production, total livestock ownerships and total income from crop production). More access to irrigation and agricultural fertilizers, improved varieties of crops, small family size, improve farmland ownership size, more access to education and Agricultural Extension services are an effective areas of intervention to improve household’s resilient, reduce households vulnerability level to climate change impacts and increase household’s total agricultural production.
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome

Significance The discovery that more than 40% of the eukaryotic proteome is intrinsically disordered, and that these disordered segments are enriched in phosphorylation sites, suggests that conformational heterogeneity may be important to kinase selectivity. Indeed, phosphorylation prediction programs reliant on classic notions of conserved sequence information (i.e., “vertical information”) are only partially effective. We find that the conformational equilibrium of the phosphorylatable site, whose information is embedded in sequence-averaged energetic and structural properties of the protein (i.e., “horizontal information”), plays a major role in distinguishing phosphorylatable versus nonphosphorylatable sites. In fact, employing both horizontal and vertical information produces a state-of-the-art phosphorylation predictor, wherein the conformational equilibrium of the disordered chain is the dominant contributor. Phosphorylation sites are hyperabundant in the eukaryotic disordered proteome, suggesting that conformational fluctuations play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural–chemical complementarity between the kinase and its protein substrates but also by the free energy difference between the conformational ensembles that are, or are not, recognized by the kinase. To test this hypothesis, we developed a statistical-thermodynamics-based informatics framework, which allows us to probe for the contribution of equilibrium fluctuations to phosphorylation, as evaluated by the ability to predict Ser/Thr/Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal information encoding substrate conformational equilibrium that is embedded, but often not apparent, within position-specific conservation patterns. We find not only that conformational fluctuations play a major role but also that they are the dominant contribution to substrate selectivity. In fact, the main substrate classifier distinguishing selectivity is the magnitude of change in local compaction of the disordered chain upon phosphorylation of these mostly singly phosphorylated sites. In addition to providing fundamental insights into the consequences of phosphorylation across the proteome, our approach provides a statistical-thermodynamic strategy for partitioning any sequence-based search into contributions from structural–chemical complementarity and those from changes in conformational equilibrium.
Collisional formation of massive exomoons of superterrestrial exoplanets

Exomoons orbiting terrestrial or superterrestrial exoplanets have not yet been discovered; their possible existence and properties are therefore still an unresolved question. Here, we explore the collisional formation of exomoons through giant planetary impacts. We make use of smooth particle hydrodynamical collision simulations and survey a large phase space of terrestrial/superterrestrial planetary collisions. We characterize the properties of such collisions, finding one rare case in which an exomoon forms through a graze and capture scenario, in addition to a few graze and merge or hit and run scenarios. Typically however, our collisions form massive circumplanetary discs, for which we use follow-up N-body simulations in order to derive lower limit mass estimates for the ensuing exomoons. We investigate the mass, long-term tidal-stability, composition and origin of material in both the discs and the exomoons. Our giant impact models often generate relatively iron-rich moons that form beyond the synchronous radius of the planet, and would thus tidally evolve outward with stable orbits, rather than be destroyed. Our results suggest that it is extremely difficult to collisionally form currently-detectable exomoons orbiting superterrestrial planets, through single giant impacts. It might be possible to form massive, detectable exomoons through several mergers of smaller exomoons, formed by multiple impacts, however more studies are required in order to reach a conclusion. Given the current observational initiatives, the search should focus primarily on more massive planet categories. However, about a quarter of the exomoons predicted by our models are approximately Mercury-mass or more, and are much more likely to be detectable given a factor 2 improvement in the detection capability of future instruments, providing further motivation for their development.
Temporal Variations in Abundance and Species Richness of Zooplankton with Emphasis on Ichthyoplankton in the Subtidal Waters of Umm Al-Namil Island, Northwestern Arabian Gulf of the ROPME Sea Area

Zooplankton, including the ichthyoplankton, abundance and species richness over time in the subtidal waters of Umm Al-Namil Island, Kuwait Bay, were sampled and quantified from September 2016 to August 2017. At the same period, physicochemical measurements (i.e., water temperature, pH, salinity, dissolved oxygen and nutrient concentrations) occurred. A total of 9 larval fish families were identified: Acropomatidae, Bregmacerotidae, Bythitidae, Clupeidae, Engraulidae, Leioganthidae, Platycephalidae, Pseudochromidae and Sparidae, in addition to fish eggs. Other zooplankton were mainly represented by Copepoda, followed by Radiolaria and Molluska larvae. Generally, some sampling events (i.e., months) had 100% fish larvae, while others had 0% fish larvae. The physicochemical parameters showed variations at each sampling event as well as within the same season. Total zooplankton (including ichthyoplankton) mean abundance was highest in summer (22.65 ± 2.85 ind.5l-1), while winter (18.13 ± 1.64 ind.5l-1) and autumn (17 ± 2 ind.5l-1) mean abundance values did not significantly vary. The lowest mean abundance was observed in spring (14.33 ± 1.67 ind.5l-1). Mean species richness was highest during spring (7.22 ± 1.66), but not significantly different from autumn (7 ± 2). No significant difference was observed between winter (6.73 ± 1.64) and summer (5.90 ± 2.85). Overall, the results indicate that zooplankton species richness and abundance in Umm Al-Namil Island varied temporally in response to fluctuations in environmental conditions. Primary among these fluctuations is water temperature at different seasons of the year.
Association between psoriasis and hepatitis B and C

Objectives: The aim of study is to assess the association between patients with psoriasis and hepatitis B and/or C. Methods: This case control study that enrolled total 110 patients with psoriasis were included in the study, 63 males and 47 females and their age range from 15 to 70 years old , with male to female ratio 1.4 :1 . The study was conducted in Al sader teaching hospital and Al Hakeem hospital in Al Najaf governorate during the period from January 2013 to February 2014. All recruited patients had their ages, gender and case histories recorded on an already prepared data sheet. All recruited patients and control groups had been subjected to that Hepatitis Bs antigen (HBsAg) and anti-hepatitis C antibodies (anti-HCV) were done using Enzyme-linked Immunosorbent Assay (ELISA) kits. Results: This study that enrolled total 110 patients were included, 63 males and 47 females and their age range from 15 to 70 years old , with male to female ratio 1.4 :1 . There were increased incidence of male patients with psoriasis 63(44.1%), but there were no statistically significant difference between studied patients and control groups, (p=0.5) . There were increased incidence of patients with psoriasis younger than 50 years, 70 (53.8%), statistically significant difference between studied patients and control groups, (p=0.007) . There were statistically significant difference between studied patients and control groups regarding smoking , 30 (33.3%), (p=0.003). There were increased incidence of seropositive for hepatitis C in patients with psoriasis . There were statistically significant difference between studied patients and control groups regarding hepatitis C 4 (16.7 %), (p=0.003). There were no statistically significant difference between studied patients and control groups regarding hepatitis B 1 (33.3%), (p=0.6) . Conclusions: This study support of an association between psoriasis and hepatitis C but not with hepatitis B. The predictors for psoriasis as risk factor in this study were male younger than 50 years with history of smoking with association with hepatitis C infection . Recommendation: Physicians who care for patients with psoriasis should be aware of this possible association and consider screening patients with psoriasis for hepatitis C infection.