Miracle-dz/UniFAR-FTUs huggingface dataset:
deGSM: memory scalable construction of large scale de Bruijn Graph

Motivation De Bruijn graph, a fundamental data structure to represent and organize genome sequence, plays important roles in various kinds of sequence analysis tasks such as de novo assembly, high-throughput sequencing (HTS) read alignment, pan-genome analysis, metagenomics analysis, HTS read correction, etc. With the rapid development of HTS data and ever-increasing number of assembled genomes, there is a high demand to construct de Bruijn graph for sequences up to Tera-base-pair level. It is non-trivial since the size of the graph to be constructed could be very large and each graph consists of hundreds of billions of vertices and edges. Current existing approaches may have unaffordable memory footprints to handle such a large de Bruijn graph. Moreover, it also requires the construction approach to handle very large dataset efficiently, even if in a relatively small RAM space. Results We propose a lightweight parallel de Bruijn graph construction approach, de Bruijn Graph Constructor in Scalable Memory (deGSM). The main idea of deGSM is to efficiently construct the Bur-rows-Wheeler Transformation (BWT) of the unipaths of de Bruijn graph in constant RAM space and transform the BWT into the original unitigs. It is mainly implemented by a fast parallel external sorting of k-mers, which allows only a part of k-mers kept in RAM by a novel organization of the k-mers. The experimental results demonstrate that, just with a commonly used machine, deGSM is able to handle very large genome sequence(s), e.g., the contigs (305 Gbp) and scaffolds (1.1 Tbp) recorded in Gen-Bank database and Picea abies HTS dataset (9.7 Tbp). Moreover, deGSM also has faster or comparable construction speed compared with state-of-the-art approaches. With its high scalability and efficiency, deGSM has enormous potentials in many large scale genomics studies. Availability https://github.com/hitbc/deGSM. Contact ydwang@hit.edu. cn (YW) and bo.liu@hit.edu. cn (BL) Supplementary information Supplementary data are available online.
Phenotypic characteristics of Indonesian native chickens

This research aimed to describe the phenotypic characteristics of local hen varieties. The study sample consisted of twenty 18 week-old hens of the following types: Cemani, black Kedu, white Kedu, and Balinese (Olagan). They were randomly selected from the "Makukuhan" farm in Kedu Temanggung, Central Java Indonesia. The results, which were analyzed using analysis of variance (ANOVA) test, showed significant differences in the quantitative characteristics of body height, body length, and tarsometatarsus length. No significant differences were found in wing length, beak length, femur length, tibiotarsus length, or body weight. Qualitative characteristics of Cemani hens differed from those of black Kedu, white Kedu, and Balinese (Olagan) hens because of their predominantly black body color. The black Kedu hens share similarities with the white Kedu hens in the colors of the tongue, comb, eyeballs, and soles of the feet. In contrast, their beak color and skin color are similar to those of the Balinese (Olagan) hens. The white Kedu hens have predominantly white feathers, and the Balinese (olagan) hens have neither comb nor neck feathers.
Assessing the Accuracy of Elementary School Test Scores as Predictors of Students' High School Outcomes. Working Paper No. 235-0520.

Testing students and using test information to hold schools and, in some cases, teachers accountable for student achievement has arguably been the primary national strategy for school improvement over the past decade and a half. Tests are also used for diagnostic purposes, such as to predict students at-risk of dropping out of high school. But there is policy debate about the efficacy of this usage, in part because of disagreements about whether tests are an important schooling outcome. We use panel data from three states – North Carolina, Massachusetts and Washington State – to investigate how accurate early test scores are in predicting later high school outcomes: 10th grade test achievement, the probability of taking advanced math courses in high school, and graduation. We find 3rd grade tests predict all of these outcomes with a high degree of accuracy and relatively little diminishment from using 8th grade tests. We also find evidence that using a two-stage model estimated on separate cohorts (one predicting 8th grade information using 3rd grade information, and another predicting high school outcomes with 8th grade information) only slightly diminishes forecast accuracy. Finally, the use of machine learning techniques increases accuracy of predictions over widely used linear models, but only marginally.
Feeding processed soybean to mid-lactation Holstein cows: ingestive behaviour and rumen fermentation characteristics

Abstract The objective of this study was to evaluate the effects of roasted soybean (RSB), extruded soybean (ESB) and their equal blend (RSB + ESB) compared with soybean meal (SBM) on nutrient intake, feed preference, meal and rumination patterns, feeding and chewing behaviour and rumen fermentation characteristics of mid-lactation dairy cows. Eight Holstein dairy cows were used in a replicated 4 × 4 Latin square design with four 28-d periods. Cows received one of the four following experimental diets: (1) 13.88% of diet dry matter (DM) as SBM; (2) 15.22% of diet DM as RSB, (3) 15.55% of diet DM as ESB and (4) 7.69% RSB plus 7.69% ESB (RSB + ESB). Each experimental period consisted of a 21-d diet adaptation period and a 7-d data collection period. Meal patterns, including meal size and inter-meal interval, were not affected by the experimental diets and thereby DM intake was not different among diets. Sorting index was not different across dietary treatments but intake of particles retained on 1.18-mm sieve and on pan increased and decreased in both SBM and ESB as compared with RSB and RSB + ESM, respectively. Total time spent eating and ruminating and rumen volatile fatty acid concentrations were unaffected by dietary treatments. Feeding processed soybean instead of SBM had minimal effects on sorting behaviour and meal patterns and thereby no changes in feed intake occurred. Finally, RSB and ESB and their equal blend had a similar effect on feed intake and chewing behaviour of mid-lactation Holstein cows. Highlights Feeding processed soybean products had the minor effect on feed intake and can be considered as alternative feedstuffs when the price is competitive.
Effects of Quarry Dust on Some Haematological Parameters among Workers at Okposi Umuoghara, Ebonyi State - Nigeria

Background: Unregulated mining has the potential to release harmful substances into the soil, air, and water and this may be associated with negative health, social and environmental impacts. Inhalable dust is produced during processing, grading and during the transit by the vehicles. Epidemiologic data indicate that there are occupational hazards associated with stone crushing and inhalation of stone dust. Quarrying/stone crushing is increasingly becoming the main stay of Ebonyi State economy and major source of internally generated revenue yet there is little or no government policy on regulation and occupational safety. Aim: This study examined the effect of long time exposure to quarry dust on the Full Blood Count (FBC) of quarry workers at Okposi Umuoghara, Ezza LGA of Ebonyi State – Nigeria. Methods: Crosssectional, descriptive and analytical study was carried out on 100 quarry workers; 36 males and 54 females (age; between 18-57 years) who were exposed to stone dust for more than one year and 84 age/sex matched workers not exposed to quarry dust as control. The haemoglobin concentration, haematocrit, total while blood cell and differential counts were estimated using standard methods. Results: Majority of the quarry workers in Okposi Umuoghara Idustrial Estate were female, low income and uneducated who are not aware of the health implications of their carrier. There were significant differences in mean values of in Hb, PCV, and total WBC, relative netrophils, lymphocytes and eosinophil counts compared with control. The differential lymphocytes and eosinophil increased significantly (p > 0.05), while the Hb, PCV, total WBC and relative neutrophil count decreased significantly (P < 0.05). No significant variation in differential monocyte count was observed. Conclusion: The alterations in level of some haemotological parameters in exposed workers is an indication of effect of quarry dust on pathopysiology of blood and reticuloendothelia system of factory workers and in general human health. There is need for regular health evaluation of workers and education on the essential safety precautions through the use of personal protective equipment and more mechanized and safer means of stone processing.
Octopods of the Canary Islands. New records and biogeographic relationships

ABSTRACT Two octopod species are reported from the Canary Islands (eastern Atlantic Ocean) for the first time: the deep sea four-horn octopus, Pteroctopus tetracirrhus (Delle Chiaje, 1830) and the gelatinous giant octopus, Haliphron atlanticus Steenstrup, 1861. Both female specimens were caught in Tenerife. Haliphron atlanticus is described from fresh remains found floating close to the southwest coast and the second species, P. tetracirrhus, is described from a specimen captured in a shrimp trap at 200 m depth on the southeastern coast of Tenerife. With these two additions the revised and updated list of octopod species of the Canary Islands now comprises eight families and 18 species, all of them incirrate octopods. The zoogeographic relationships of octopod species from other Atlantic regions, including the Mediterranean Sea, were studied. The likely directions of faunal flows were inferred based on affinity indices, showing that Mauritania could be the most probable source of the octopod species of the Canary Islands and the rest of the Macaronesian archipelagos.
Climate Variability Effects on Uruguayan Whitemouth Croaker and Striped Weakfish Fisheries

Analysis of climatic drivers effects on Micropogonias furnieri and Cynoscion guatucupa fisheries of Uruguay. Climatic and fisheries variables from the period 1982-2018 were analysed. Statistical analysis such as Wavelets Analysis and General Additive Models were performed. Results show that captures of the two species are being affected by climatic variability.
Rootstock on production and quality of ‘Niagara Rosada’ grapevine

Abtract In Brazil, the producers have changed used rootstocks to get more vigor to scion. Rootstocks change the distribution of bud fruitfulness over grapevine shoots and the expression of the bud fruitfulness into fruit yield. Hence, these modification could alter ideal pruning length. In this way, it was evaluated bud fruitfulness, fruit yield and quality of ‘Niagara Rosada’ grapevine grafted onto rootstocks: ‘IAC 766’, ‘IAC 572’, ‘IAC 313’, ‘IAC 571-6’, and ‘Riparia do Traviu’, which ‘IAC 766’ is the most used rootstock in São Paulo State, nowadays. The evaluations were performed over three crop seasons, in a vineyard located in Louveira, SP. Two evaluations were performed in Brazilian traditional season, and one crop pruning was performed in Brazilian summer, called “off-season”. In traditional seasons, the bud fruitfulness was evaluated from the first to fourth bud in 2014 and to the fifth in 2015. In the off-season, bud fruitfulness was evaluated from the fifth to eighth bud. Fruit yield and quality were also evaluated over the three production cycles. Bud fruitfulness of ‘Niagara Rosada’ grafted onto the evaluated rootstocks showed that this characteristic was more affected by the environmental conditions, confirmed due to alteration of bud fruitfulness through production cycles. Additionally, no effect of rootstock was observed on fruit yield, and quality of ‘Niagara Rosada’. Only isolated variations were detected, and these are not enough to confirm the influence of rootstocks on scion of ‘Niagara Rosada’. Although no effect of rootstocks on bud fruitfulness, fruit yield and quality has been observed in the evaluated conditions, all rootstocks are recommended to be used in combination with ‘Niagara Rosada’.
Determination of the Upper Limit Age of Jatropha Curcas Plantation for Optimum Yield Production

Jatropha curcas (L.) provenances were grown to determine the upper limit age for maximum seed yield production. The study had been conducted at Shewa robit district in the lowland areas of the North Shewa zone. In this study, fourteen Jatropha curcas provenances had been collected from different parts of Ethiopia. Sixteen plants per plot had been planted in a randomized complete block design with three replications. The survival rate, number of branches, seed yields and growth parameter data had been collected from those plants. Survival rate ranged from 85-100%; root collar diameter was ranged between11.80 cm and 13.51 cm at the age of six years. The maximum and minimum plant heights were 281.96 cm and 233.88 cm, respectively, at the age of five years after planting. Those different traits of Jatropha curcas indicated that statistically insignificant difference (p>0.05) except the seed yield of Cheffa provenance was significantly highest at the age of four years. The maximum seed yield (cheffa) was 38.837 ton/ha/year, and the minimum was 9.016 ton/ha/year (Jewuha) within the same year. All Jatropha curcas provenances seed yield was maximum at the age of four years and declined after six years of age.
Immunological activities of polysaccharide extracted from Elaeagnus angustifolia L.

ABSTRACT The study was to investigate the immunological activities of polysaccharide isolated from Elaeagnus angustifolia L. The extracted Elaeagnus angustifolia L. polysaccharide (EAP) was purified by DEAE cellulose-52 chromatography (DEAE-52) and Sephadex G-100 size-exclusion chromatography (G-100). Then the average molecular weight (Mw) of purified polysaccharide was determined by high-performance gel permeation chromatography (HPGPC). One main fraction (EAP-1a) was obtained through the isolation and purification steps. The results showed that EAP-1a had strong immunological activities. EAP-1a could significantly increase spleen and thymus index, enhance the NK cell activity, stimulate the phagocytosis of peritoneal phagocyte and increase the level of IL-2, IFN-γ and IgG in serum. Thus, EAP-1a isolated from Elaeagnus angustifolia L. could enhance the immunological activities of immunosuppressed mice induced by cyclophosphamide (CY).
Chemical speciation and health risks of airborne heavy metals around an industrial community in Nigeria

Abstract Quantification of PM2.5 (particulate matter <2.5 µm) bound heavy metals and their potential health risks were carried out around a cement manufacturing company in Ewekoro, Nigeria. The PM2.5 samples were collected using Environtech gravimetric sampler. A four-staged sequential extraction procedure was used to fractionate PM2.5 bound chromium (Cr), lead (Pb), aluminum (Al), copper (Cu), and silver (Ag), and further analyzed using inductively coupled plasma mass spectrometry. Chemical speciation results reveal bioavailable levels of Pb (4.05 µg/m3), Cr (10.75 µg/m3), Al (16.47 µg/m3), Cu (4.38E-01 µg/m3), and Ag (1.22E-02 µg/m3) in the airborne particulates. Pb and Cr levels exceeded the World Health Organization allowable limit of 0.5 and 2.5E-05 µg/m3, respectively. The labile phases showed strong indication of the presence of Cr and Cu metal. Excess cancer risks exposure for adults, outdoor workers and children were higher than the acceptable risk target level of 1E-06. Non-carcinogenic health risk estimated using hazard quotients (HQs) and hazard indices (HIs) showed ingestion route within the safe level of HI <1 implying no adverse effect while inhalation route exceeded the safe level for all receptors. Enforcement of pollution control by authorized agencies, and screening of greenbelts as sinks for air pollutants is strongly recommended.
Spatiotemporal Analysis of Vegetation Cover Change in a Large Ephemeral River: Multi-Sensor Fusion of Unmanned Aerial Vehicle (UAV) and Landsat Imagery

Ephemeral rivers in arid regions act as linear oases, where corridors of vegetation supported by accessible groundwater and intermittent surface flows provide biological refugia in water-limited landscapes. The ecological and hydrological dynamics of these systems are poorly understood compared to perennial systems and subject to wide variation over space and time. This study used imagery obtained from an unmanned aerial vehicle (UAV) to enhance satellite data, which were then used to quantify change in woody vegetation cover along the ephemeral Kuiseb River in the Namib Desert over a 35-year period. Ultra-high resolution UAV imagery collected in 2016 was used to derive a model of fractional vegetation cover from five spectral vegetation indices, calculated from a contemporaneous Landsat 8 Operational Land Imager (OLI) image. The Normalized Difference Vegetation Index (NDVI) provided the linear best-fit relationship for calculating fractional cover; the model derived from the two 2016 datasets was subsequently applied to 24 intercalibrated Landsat images to calculate fractional vegetation cover for the Kuiseb extending back to 1984. Overall vegetation cover increased by 33% between 1984 and 2019, with the most highly vegetated reach of the river exhibiting the greatest positive change. This reach corresponds with the terminal alluvial zone, where most flood deposition occurs. The spatial and temporal trends discovered highlight the need for long-term monitoring of ephemeral ecosystems and demonstrate the efficacy of a multi-sensor approach to time series analysis using a UAV platform.
Non-Audit Services in Audit Committee Interlocked Firms, Financial Reporting Quality, and Future Performance

We investigate whether board-interlocked firms via an audit committee (AC) board member exhibit correlated non-audit service (NAS) purchases, and whether financial reporting quality and future firm performance vary with the amount of correlated NAS purchases from the AC interlock. We find that AC interlocked firms have positively correlated total NAS and three NAS subtypes—Tax, Assurance, and Other—in the overall sample period from 2000 to 2016, and in each of the subperiods pre- and post-SOX (Sarbanes–Oxley Act). Firms with a larger NAS component that is explained by the AC interlock tend to exhibit lower financial reporting quality. We also find evidence that firms with higher AC interlocked NAS purchases are associated with lower future performance, although this association exists only in the pre-SOX period. Overall, the evidence suggests that greater NAS purchases among AC interlocked firms can have a detrimental effect on financial reporting quality and auditor independence. While these detrimental effects are concentrated in the pre-SOX period when there were less restrictions on NAS purchases, we find some evidence that the association with lower financial reporting quality persists in the post-SOX period.
ANALISIS PENGARUH CURRENT RATIO, DEBT RATIO, DEBT TO EQUITY RATIO TERHADAP RETURN ON INVESTMENT PADA PERUSAHAAN PERTAMBANGAN DI BURSA EFEK INDONESIA

Tujuan dari penelitian ini adalah untuk mengetahui dan menganalisis pengaruhCurrent Ratio, Debt Ratio, Debt To Equity Ratio, terhadap Return On Investment baik secaraparsial maupun simultan. Populasi dalam penelitian ini adalah perusahaan petambangan yangterdaftar di Bursa Efek Indonesia untuk periode 2014-2018. Dengan menggunakan teknikpengambilan sampel (purposive sampling) diperoleh sebanyak 8 perusahaan yang akandijadikan sebagai objek penelitian. Metode pengujian untuk melihat pengaruh variabelindependen terhadap variabel dependen adalah metode analisis regresi linier berganda.Berdasarkan hasil penelitian secara parsial, hanya Current Ratio dan Debt Ratio yangberpengaruh signifikan terhadap Return On Investment, sedangkan Debt to Equity Ratio tidakberpengaruh signifikan terhadap Return On Investment. Secara simultan diketahui bahwaCurrent Ratio, Debt Ratio, Debt to Equity Ratio, berpengaruh signifikan terhadap Return OnInvestment.
Nest survival, causes of failure and productivity of British Hawfinches Coccothraustes coccothraustes

ABSTARCT Capsule: Nest success rate of Hawfinches Coccothraustes coccothraustes within our study areas averaged 36% across five seasons, a level unlikely to be driving population declines and considerably higher than was suggested by recent estimates from the long-term Nest Record Scheme. Aims: To investigate potential habitat correlates of nest success and identify nest predators from an intensive study on Hawfinches. To compare nest success and habitat of these nests with those found by Nest Record Scheme (NRS) recorders and test whether there is evidence of a decline in nest success over time from the NRS data. Methods: Females trapped at feed sites were fitted with radio-tags and tracked back to nest sites providing a sample of nests for subsequent monitoring. Habitat measures potentially influencing survival were collected at nest sites and modelled against nest outcome. Nest success was compared with that from the long-term Nest Record Scheme. Nest cameras were deployed to identify predators. Results: Nest success varied among years, but the mean value was not substantially lower than other Hawfinch studies or from other species with similar nesting strategies. Apparent recent declines in success suggested by Nest Record Scheme data were not evident in our study areas. Only avian species were recorded predating nests and a number of partial predations were recorded. No correlation was found between overall success for study nests and the habitat or temporal measurements collected. Conclusions: Within our study areas, average Hawfinch nest success and productivity appeared to be sufficient to maintain local population stability though our sample size was modest and further work would be beneficial. General nest recording may have inherent biases that lead to an over-estimation of nest failure compared to those found by more structured study. Drivers of recent UK Hawfinch declines may be operating outside of the nesting season and/or in landscapes outside primary woodland.
Physiological and protein responses in leaves of Nitraria billardieri seedlings to moderate salt stress

ABSTRACT Salt stress is a major environmental factor affecting plant growth and geographical distribution. Halophytes are considered valuable resources for investigating plant tolerance mechanisms. The halophyte Nitraria billardieri is widely distributed in saline soil in Australia and China. To investigate salt stress-induced changes at the physiological and molecular levels in N. billardieri, three-month-old seedlings were subjected to salt stress treatments. The physiological and biochemical analyses showed that N. billardieri seedlings could adapt to and strongly tolerate salt stress by accumulating soluble sugars and proline as organic osmolytes and increasing the activities of antioxidative enzymes. Comparative proteomic and metabolic pathway analyses revealed 130 differentially expressed proteins, which displayed various response patterns under salt stress. A protein interaction analysis found that the interaction consisting of amino acid and carbohydrate metabolism coupled with redox homeostasis and protein synthesis may play an essential role in response to salt stress in N. billardieri seedlings. Overall, salt stress treatment disrupted a cascade of normal metabolic programing and subsequently caused oxidative and osmotic stress by altering protein fates, signal transduction and redox homeostasis.