bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minor QTLs mining through the combination of GWAS and machine learning feature selection
Authors: Zhou Wei , Bellis Emily S. , Stubblefield Jonathan , Causey Jason , Qualls Jake , Walker Karl , Huang Xiuzhen 
Published: May 2019

Abstract
Background

Minor QTLs mining has a very important role in genomic selection, pathway analysis and trait development in agricultural and biological research. Since most individual loci contribute little to complex trait variations, it remains a challenge for traditional statistical methods to identify minor QTLs with subtle phenotypic effects. In this study, we developed a new framework which combined the GWAS analysis and machine learning feature selection to explore new ways for minor QTLs mining.

Results

We studied the soybean branching trait with the 2137 accessions from soybean (Glycine max) diversity panel, which was sequenced by 50k SNP chips with 42,080 valid SNPs. First as a baseline study, we conducted the GWAS GAPIT analysis, and we found that only one SNP marker significantly associated with soybean branching was identified. We then combined the GWAS analysis and feature importance analysis with Random Forest score analysis and permutation analysis. Our analysis results showed that there were 36077 features (SNPs) identified by Random Forest score analysis, and 2098 features (SNPs) identified by permutation analysis. In total, there were 1770 features (SNPs) confirmed by both of the Random Forest score analysis and the permutation analysis. Based on our analysis, 328 branching development related genes were identified. A further analysis on GO (gene ontology) term enrichment were applied on these 328 genes. And the gene location and gene expression of these identified genes were provided.

Conclusions

The combined GWAS and feature selection with machine learning methods provide a new analysis framework, which shows significant identification power for minor QTLs mining. This research on minor QTLs mining helps to understand the biological activities that lies between genotype and phenotype in terms of causal networks of interacting genes. This research also provides an integrative approach for effective genomic selection in plant breeding and help broaden the way of molecular breeding in plants.
Study of the Efficiency and Workflow of Femtosecond Laser-Assisted Cataract Surgery in a Spanish Public Hospital
Authors: Villavilla-Castillo Jacinto , de Mora Marina Rodríguez Calvo , Pérez-Casaseca Cristina , de-los-Riscos Emilio Espejo , Baca Gustavo Fernandez , Fernández-Baca-Casares Ildefonso , Piñero-Llorens David P. 
Published: May 2019

Abstract
Background: To assess the time-efficiency of a designated operation room (OR) workflow in the introduction of Femtosecond laser-assisted cataract surgery (FLACS, LenSx, Alcon®). The study was carried out in a public hospital with high volume of procedures.
Methods: We performed this prospective, controlled, surgical intervention study in the Ophthalmology department of a tertiary referral Spanish public hospital. A total of 167 eyes were enrolled, including 62 eyes undergoing conventional phacoemulsification surgery. In phase I, patients were assigned either to FLACS-I (n=63) or conventional phacoemulsification surgery (n=62). One surgeon operated the Femto-second laser, another finished the procedure, whereas another performed a conventional phacoemulsification. In the second phase (FLACS-II), all the surgeries were FLACS (n=42). A surgeon performed the FLACS procedure and two different surgeons completed the surgeries in separated ORs. Surgical and roll-over times of all the patients were recorded.
Results: Preparation time was statistically significant lower in FLACS-I and FLACS-II (p<0.001) whereas the time of the cataract procedure per se was higher in FLACS-II compared to conventional phacoemulsification (p= 0.03). Phacoemulsification energy was higher in FLACS-II compared to FLACS-I (p = 0.01) whereas laser-related surgical time was lower (p = 0.001). Surgical complications and total surgical time showed no statistically significant differences between all three groups.
Conclusions: This study suggests a time-efficient and suitable workflow model for FLACS considering the specific requirements and restrictions of a saturated public hospital. Even so we have shown that FLACS procedure does not take longer than conventional phacoemulsification following a detailed planning for the OR workflow. Besides, our data reflect an improvement surgical times in FLACS with ongoing experience.
Trial registration: NCT03931629 (retrospectively registered)
Purtscher-like retinopathy presented a honeycomb-like pattern in optical coherence topography angiography
Authors: Li Bing , Chen Youxin , Li Donghui 
Published: May 2019

Abstract
Background
To report a case of Purtscher-like retinopathy (PUR) and his optical coherence tomography (OCT) and OCT-angiography (OCT-A) findings before and after treatment.

Case presentation
A 65-year-old male presented with acute onset of vision loss for 2 weeks. Fundus examination revealed cotton-wool spots, retinal hemorrhage, and purtscher flecken spreading around the optic disc in the right eye. He was diagnosed with Purtscher-like retinopathy because of the absent reports of any traumatic medical history. OCT presented some band-like hyperreflective lesions at the layer of inner nuclear layer known as paracentral acute middle maculopathy (PAMM). OCT-A revealed apparent reduction of blood flow signal at the layers of deep retina and choriocapillaris with a pattern of honeycomb-like hypointense signal. After 3-month follow-up, OCT scan showed a resolution of retinal edema, but the PAMM lesions were still visible. OCT-A presented the honeycomb-like pattern turned into a homogeneous reduction of blood flow with small patches of hypointense signal areas in choriocapillaris.

Conclusion
This case presented a new OCT-A sign in Purtscher-like retinopathy with a honeycomb-like hypointense signal at the layer of choriocapillaris indicates the involvement and the ischemia condition of the choroid in its pathological process.
Estimation of the adaptive capacity of Schisandra chinensis to drought
Authors: Н. В. Скрипченко  , Г. В. Слюсар  
Published: May 2019

Рurpose. The determination of adaptive ability of Schisandra chinensis (Turcz.) Baill plants to drought under the conditions of introduction in the M. M. Gryshko National Botanical Garden of the National Academy of Sciences of Ukraine on the basis of study of morpho-anatomical and biochemical features of the leaves. Methods. The anatomical structure of S. chinensis leaves was studied by light microscopy using fresh and dried raw materials. The water retention capacity was determined by laboratory method according to the rate of water loss and the degree of damage to isolated leaves. The dynamics of the content of pigments in S. chinensis leaves was determined by the spectrophotometric method during the vegetation period. Results. Certain morpho-anatomical signs of S. chinensis leaves contributing to plant resistance to conditions with high air temperature and water deficiency were identified – the presence of a wax layer on the surface of the epidermis and cuticle, calcium oxalate crystals and secretory cells. According to the scale of the parameters of water regime of leaves, the studied plants are characterized by high level of adaptation to drought too. It was revealed that the pigment complex of leaves is sensitive to changes in the environmental factors. The content of pigments in the plant leaves varies with changes in hydrothermal conditions of growth. The dynamics of the content of chlorophylls and carotenoids is related to the physiological state of plants and to a certain degree characterizes their adaptive potential. Conclusions. The results of morpho-structural studies of S. chinensis leaves and their water-physical properties indicate a high level of adaptability of plants to environmental stressors such as insufficient water supply and high temperature. S. chinensis plants can be recommended for widespread introduction into garden cenosis for obtaining valuable fruit and medicinal raw materials.
Adaptability of potato varie­ties to soil-climatic conditions of the Polissia and Forest-Steppe zone of Ukraine
Authors: Т. Д. Сонець  , З. Б. Києнко  , М. М. Фурдига  , Ю. Я. Верменко  
Published: May 2019

Purpose. To define the main criteria for adaptability and determine the adaptive capacity of different varieties of potatoes tested in Polissia and Forest-Steppe of Ukraine for use in seed production. Methods. The productive potential of potato varieties to determine overall species adaptability was analyzed in terms of yield. For this purpose, the coefficient of adaptability of varieties (CA) was used determined by their yield in the year of cultivation in ratio to the ave­rage yield of the year. Results. Over the years of research (2014–2016), under similar conditions of cultivation, the varieties responded in different ways to conditions of the environment in relation to the year of testing. The overall CA of 1.0 and higher indicates increased adaptability of the variety in the soil and climatic conditions of the growing area to changes in weather conditions during the growing season. In particular, in Polissia these are ‘Esmi’ (CA 1.12), ‘Catania’ (CA 1.06), ‘Constans’ (CA 1.03); in the Forest-Steppe – ‘Esmi’ (CA 1.16), ‘Catania’ (CA 1.12), ‘Constans’ (CA 1.00). Specific adaptive ability of varieties is manifested in high average variety yields in years favorable by weather conditions for potato cultivating. The increase in the yield of such varieties in Polissia was 0.4–1.9 t/ha, in the Forest-Steppe – 0.7–2.8 t/ha. ‘Esmi’, ‘Catania’, ‘Yavir’, ‘Constans’ belong to such varieties in Polissia, ‘Esmi’, ‘Catania’, and ‘Constans’ – in the Forest-Steppe. Conclusions. The use the coefficient of adaptability allows determining the productive capacity of a variety in specific soil and climatic conditions. The cultivation of potato varieties with increased adap­tability is a significant factor in increasing the production of high-yielding potato varieties, primarily seed material of high categories for varieties rotation and replacement. In particular, according to research results, such varieties of potatoes in Polissia and Forest-Steppe conditions are ‘Esmi’, ‘Catania’ and ‘Constans’.
An Assessment of the Contact History of Multi-Drug Resistant Tuberculosis Patients from Sindh: A Gender based comparison
Authors: Noori Muhammad Yahya , Rizwan Saharish , Ali Zaheer , Sharafat Shaheen 
Published: May 2019

The purpose of this project was to evaluate the pattern of transmission in patients suffering from Multidrug resistant (MDR) Tuberculosis by assessing their contact information. Data were obtained and analyzed from 164 individuals suffering from MDR TB. Records were scanned to evaluate the presence ofa close contact with known history of Tuberculosis. Tabulations and analysis were performed in Microsoft Excel® and online calculators. Analysis of contact data showed that only 36% of the patients had a close contact with a known Tuberculosis patient. Chi-square test did not show any association between history ofpresence of a contact and the patients’ gender (p>0.5). Among the cases with established exposure with a TB patient among close contacts, 17.5% females and 12.5% males reported exposure with a contact outside the close family. Majority of patients were unaware of the presence of a known contact in their vicinity. There was no association between knowledge about exposure and patients’ gender. The study shows that efforts of active case finding should be employed to find the hidden cases of Tuberculosis in the society to stop the spread by those patients, who are unaware of their disease.
Comparison of Letrozole versus Danazol for the Pain Management of Females Presented with Endometriosis
Authors: Rasul Sadaf Ghulam , Yaqub Uzma , Manzoor Maida , Mubasshar Hafsa 
Published: May 2019

Endometriosis is an estrogen-regulated disease, and is signified by the existence of a particular endometrial tissue exterior to the uterus. It is a principal cause of long lasting morbidity, mostly from serious pelvic pain(1). Endometriotic tissue has the potential for aromatase gene expression that leads to aromataseand estrogen production. Danazol is a synthetic androgen whereas Letrozole is aromatase inhibitor. This study was conducted to compare the mean decrease in visual analogue scale (VAS) pain score with Danazol versus Letrozole for the pain management of endometriosis in females. A total of 140 females fulfillinginclusion criteria were registered and an non-probability purposive technique of sampling was used. Diagnostic laparoscopy was conducted to make a diagnosis of endometriosis. Females were divided into two groups. Females in group A received treatment with Letrozole tablets (2.5 mg/day) and in group B receivedDanazol tablets (600 mg/day) for 3 months. Pelvic pain was assessed using VAS score and the mean decrease in pain score was assessed between two groups using independent sample student t-test. Results of this study demonstrate that the mean age of the patients was 29.99±5.80 and the mean pain score before treatment in Letrozole group was 3.04±1.01 while in Danazol group was 5.05±1.02. Post-three months of treatments, mean pain score was 2.01±0.95 and 2.78±0.99 in Letrozole and Danazol groups, respectively. The mean decrease in pain score in Letrozole group was 1.02±1.09 (p-value=0.00) while in Danazol group; it was 3.06±1.23 (p-value=0.00). This difference in pain score was considerably different in both treatment groups. A higher decrease in pain score was observed in Danazol compared to Letrozole treated groups.
Enhancing efficiency and economics of phosphorus recovery process by customizing the product based on sidestream characteristics – an alternative phosphorus recovery strategy
Authors: Shaddel Sina , Ucar Seniz , Andreassen Jens-Petter , Østerhus Stein W. 
Published: May 2019

Abstract
The enhanced biological phosphorus removal process makes the phosphorus recovery feasible from the dewatering streams of biological sludge. The physicochemical properties of these sidestreams, as an input to a crystallizer, are different before and after anaerobic digestion. In this study, phosphorus recovery by calcium phosphate is proposed for pre-digestion sidestreams and by struvite precipitation for post-digestion sidestreams. The thermodynamic modeling followed by experimental tests was performed to evaluate the recovery efficiency and product properties of struvite and calcium phosphates. The variations in phosphorus recovery potential, reaction kinetics and particle size distribution emphasize the importance of the adjustment of initial supersaturation and pH of the reaction. The optimum pH, considering the economics and recovery efficiency, for both calcium phosphate and struvite precipitation was found to be pH = 8.5, whereas further increase of pH will not improve the overall efficiency of the process. In the case of calcium phosphate precipitation, it was shown that possible phase transformations should be considered and controlled as they affect both process efficiency and product properties. The economic evaluation indicated that the optimized operational condition should be determined for the phosphorus recovery process and that chemical costs for the production of calcium phosphates is lower than for struvite.
The Importance of Precision Medicine in Type 2 Diabetes Mellitus (T2DM): From Pharmacogenetic and Pharmacoepigenetic Aspects
Authors: Khatami Fatemeh , Mohajeri-Tehrani Mohammad R. , Tavangar Seyed M. 
Published: May 2019

Background:Type 2 Diabetes Mellitus (T2DM) is a worldwide disorder as the most important challenges of health-care systems. Controlling the normal glycaemia greatly profit long-term prognosis and gives explanation for early, effective, constant, and safe intervention.Materials and Methods:Finding the main genetic and epigenetic profile of T2DM and the exact molecular targets of T2DM medications can shed light on its personalized management. The comprehensive information of T2DM was earned through the genome-wide association study (GWAS) studies. In the current review, we represent the most important candidate genes of T2DM like CAPN10, TCF7L2, PPAR-γ, IRSs, KCNJ11, WFS1, and HNF homeoboxes. Different genetic variations of a candidate gene can predict the efficacy of T2DM personalized strategy medication.Results:SLCs and AMPK variations are considered for metformin, CYP2C9, KATP channel, CDKAL1, CDKN2A/2B and KCNQ1 for sulphonylureas, OATP1B, and KCNQ1 for repaglinide and the last but not the least ADIPOQ, PPAR-γ, SLC, CYP2C8, and SLCO1B1 for thiazolidinediones response prediction.Conclusion:Taken everything into consideration, there is an extreme need to determine the genetic status of T2DM patients in some known genetic region before planning the medication strategies.
Utility of Plasma Concentration of Trimethylamine N-Oxide in Predicting Cardiovascular and Renal Complications in Individuals With Type 1 Diabetes
Authors: Winther Signe A. , Øllgaard Jens C. , Tofte Nete , Tarnow Lise , Wang Zeneng , Ahluwalia Tarunveer S. , Jorsal Anders , Theilade Simone , Parving Hans-Henrik , Hansen Tine W. , Hazen Stanley L. , Pedersen Oluf , Rossing Peter 
Published: May 2019

OBJECTIVE
Trimethylamine N-oxide (TMAO) is suggested as an independent gut microbiota–derived risk factor for cardiovascular and renal disease. We investigated associations between plasma TMAO concentrations and cardio-renal outcomes in a prospective study of individuals with type 1 diabetes.

RESEARCH DESIGN AND METHODS
Plasma TMAO was measured at baseline in 1,159 individuals with type 1 diabetes (58% male, mean ± SD age 46 ± 13 years). End points were all-cause and cardiovascular mortality, cardiovascular disease (CVD), and renal events tracked from national registries. Associations between TMAO and end points were tested using Cox regression models.

RESULTS
After 15.0 (6.7–19.3) (median [interquartile range]) years of follow-up, we recorded all-cause and cardiovascular mortality (n = 363 and 120, respectively), combined CVD (n = 406), coronary outcome (myocardial infarction and coronary intervention) (n = 163), stroke (n = 115), hospitalization for heart failure (n = 81), and end-stage renal disease (n = 144). In univariate analyses, higher TMAO concentrations were associated with all end points (P ≤ 0.005). Except for stroke and heart failure, all end points remained significantly associated with higher TMAO concentrations after adjustment for conventional cardiovascular risk factors (P ≤ 0.003). After further adjustment for baseline estimated glomerular filtration rate (eGFR), results became insignificant for all end points. TMAO was inversely associated with baseline eGFR (R2 = 0.29; P &lt; 0.001).

CONCLUSIONS
In individuals with type 1 diabetes, higher concentrations of plasma TMAO were associated with mortality, CVD events, and poor renal outcome, independent of conventional risk factors. However, the association became insignificant after further adjustment for baseline eGFR. This could reflect TMAO as a renal function marker or a risk factor for micro- and macrovascular complications mediated through impaired renal function.
Uji Aktivitas Antibakteri Ekstrak Etanol Bawang Dayak (Eleutherine palmifolia (L.) Merr) Terhadap Bakteri Staphylococcus aureus
Authors: Warsiti Warsiti , Wardani Sisca Dwikusuma , Ramadhan Ardea Achmad , Yuliani Ratna 
Published: May 2019

Staphylococcus aureus is an infectious bacteria with pus because of tissue damage. Infectious diseases caused by S. aureus include wound infections, ulcers, pimples, and impetigo. Dayak onions have the benefit of being antibacterial. This research aims to study the antibacterial activity of ethanolic extract of Dayak onions against Staphylococcus aureus. The antibacterial study was carried out using the disk diffusion method. Identification of bacteria by Gram staining showed Gram-positive bacteria which can ferment mannitol with the mannitol test. A bacterial sensitivity test was conducted using three antibiotics i.e. cefoxitin 30μg, vancomycin 30μg, and linezolid 30μg. The bacteria was sensitive to all of the three antibiotics, with the inhibitory zone of 23.5 mm; 17 mm and 27.5 mm, respectively. Vancomycin 30μg was used as a positive control, resulted in average diameter of the inhibitory zone of 17.83 2.25 mm, whereas a control solvent DMSO (Dimethyl sulphoxide) did not produce zones. The ethanolic extract of Dayak onion in the concentration of 25%; 50%; 75% and 100% showed the average diameter of inhibitory zones of 8.17 0.29 mm; 10.67 1.44 mm; 10.33 1.53 mm; and 12.33 1.61 mm, respectively
PERANAN POLRI DALAM PERLINDUNGAN TERHADAP SAKSI DAN KORBAN PADA PROSES PERKARA PIDANA
Authors: Suyoto Suyoto 
Published: May 2019

Lahirnya Undang-Undang Perlindungan Saksi dan Korban dianggap sangat penting dalam rangka perlindungan saksi dan korban terhadap hak- hak individunya. Kedudukan saksi dalam proses perkara pidana menempati posisi kunci. Posisi penting yang dimiliki oleh saksi dalam proses perkara pidana, maka sudah menjadi kewajiban bagi aparat penegak hukum, khususnya aparat kepolisian untuk memberikan perlindungan saksi dan korban. Perlindungan saksi tersebut merupakan bagian dari tugas pokok lembaga kepolisian dalam rangka memelihara keamanan dan ketertiban (peace and order maintenance) dan penegakan hukum (law enforcement).Undang-undang perlindungan saksi dan korban merupakan karya terbaru bangsa dalam perkembagan hukum pidana Indonesia yang mengilhami sebuah cita-cita hukum yang melindungi hak asasi segenap bangsa Indonesia terutama hak saksi dan korban dalam proses peradilan pidana. Menilik pentingnya saksi sebagaimana ditegaskan dalam ketentuan Pasal 184 – Pasal 185 KUHAP, maka sudah sewajarnya saksi atau korban dalam upaya penegakan hukum diberikan perlindungan, sehingga dalam memberikan kesaksiannya di depan pengadilan, saksi merasa aman dan bebas dari ancaman / tekanan baik fisik atau psikis terhadap diri dan keluarganya.Sasaran perlindungan yang diberikan Undang-Undang No.13 Tahun 2006, terhadap saksi dan korban diatur dalam Pasal 5 bahwa hak yang diberikan kepada saksi dan/atau korban tindak pidana dalam kasus-kasus tertentu sesuai dengan keputusan Lembaga Perlindungan Saksi dan Korban. Pasal 36 ayat (1) Undang-Undang No.13 Tahun 2006, memberikan mandat kepada Lembaga Perlindungan Saksi dan Korban untuk bekerjasama dengan instansi berwenang lainnya yang terkait. Perlindungan hukum terhadap saksi oleh pihak POLRI dilakukan berdasarkan tugasnya yang diatur dalam ketentuan Pasal 2, Pasal 13 sampai dengan Pasal 15 Undang-Undang Nomor 2 Tahun 2002 tentang Kepolisian Negara Republik Indonesia. Perlindungan hukum diberikan agar saksi dan korban dapat memberikan kesaksian dengan sebaik-baiknya.
Proverbs as a Means of Crossing Cultural Borders
Authors: Buja Elena 
Published: May 2019

Abstract
“The grass is always greener on the other side of the fence/hill” is an old English proverb which shows that people tend to appreciate more what others have, just by crossing (with their eyes) the border represented by the fence/hill. Though the afore-mentioned proverb is a strong piece of advice against comparing what we possess with what others have, the aim of my paper is exactly that: to compare proverbs belonging to the Romanian culture to those of the Korean one, not for the sake of highlighting the wisdom or beauty of the Romanian over the Korean proverbs or vice versa but rather for identifying similarities and differences in terms of structure, vocabulary, and, above all, meaning, being aware that proverbs are elements of language that best reflect a culture’s beliefs and values. To this aim, 50 Romanian proverbs selected from two memorable Romanian sources (Iordache Golescu’s Proverbe comentate ‘Commented Proverbs’ and Anton Pann’s Proverbele românilor ‘The Romanians’ Proverbs’) will be compared with their Korean counterparts.