bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China
Authors: Hou Wanwei , Zhang Xiaojuan , Liu Yuling , Liu Yujiao , Feng Bai li 
Published: January 2023

Background
Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.

Methods
Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.

Results
A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.
Distribution of Cowries in the Different Ecological Habitats in the Selected Sites in Davao Occidental
Authors: Caalim Lorah May C. , Catulinan Diego G. , Elemino Michelle M. 
Published: January 2023

Aims: The primary aim of this study was to assess the species of cowries in the different ecological habitats of Barangay Buhangin, Tubalan, and Tanglad, Davao Occidental. Specifically, it sought to identify species of cowries found in the study area, population density, abundance, and diversity.
Place and Duration of Study: Barangay Buhangin, Tubalan, and Tanglad, Davao Occidental, April 10 – 30, 2022.
Methodology: The study employed a transect-line-quadrat method. There were three stations were established in the selected areas. The quadrat was used to determine the density, abundance, dominance, and diversity of cowries. A 1m x 1m quadrat was thrown randomly on the established layout of 50 ㎡ (25m x 2m) parallel to the shore. Gears, such as diving goggles and snorkel were used to determine the cowries inside the quadrat and were hand-picked for species identification.
Results: The study revealed that there were ten (10) species of cowries recorded and identified. In Station 1 (Barangay Buhangin), seven species were found namely: Monetaria annulus (Gold ring cowry), Cypraea tigris (Tiger cowry), Mauritia arabica (Arabian cowry), Monetaria caputserpentis (Serpent’s head cowry), Naria erosa (Eroded cowry), Monetaria moneta (Money cowry) and Luria isabella (Fawn-coloured cowry). In Station 2 (Barangay Tubalan) two species were recorded and identified, namely: Cypraea tigris (Tiger cowry) and Mauritia arabica (Arabian cowry), while in Station 3 (Barangay Tanglad), eight species were recorded and identified, these were: Monetaria annulus (Gold ring cowry), Cypraea tigris (Tiger cowry), Mauritia arabica (Arabian cowry), Naria erosa (Eroded cowry), Monetaria moneta (Money cowry), Lyncina vitellus (Calf cowry), Lyncina lynx (Eyed cowry), and Palmadusta asellus (Littleass cowry). In Station 1, Coral Reef Habitat has the most diverse species with five (5) species found, while the seagrass bed habitat is the most abundant in terms of population with nine (9) cowries found, and the mangrove habitat only houses one (1) species of cowry with a population of three (3).
Conclusion: Station 3 was the most diverse in terms of cowry species with 8 species identified. Station 1 and Station 2 have the highest population of juvenile cowry species with a total of 127 juvenile species, and Station 2 has the highest population of adult cowry species with a total of 17 adult species. There were four (4) cowry species found in the mangrove habitat, four (4) cowry species were also found in the seagrass bed habitat and nine (9) cowry species were found in the coral reef habitat thus making it the most diverse among all ecological habitats.
Modification of Protein Hydrolyzate of Snakehead Fish as an Ingredient for Instant Seasoning Coto Makassar
Authors: Tartar Sri Udayana , Fitri Muhammad , Syukroni Ikbal 
Published: January 2023

Aim: This study aimed to determine the ratio formula for the hydrolyzate of snakehead fish head flour and Instant seasoning flour of Coto Makassar.
Study Design: The experimental design used was using an independent t test (independent t-test) namely (Coto Seasoning Flour: HPKIG Flour) / (TC: THPKIG) as follows A = (TC: THPKIG) = 90% : 10% (b /b) and B= (TC: THPKIG) = 80% : 20% (w/b).
Place and Duration of Study: The research had carried out from May 2018 to August 2019, the production of the hydrolyzate of snakehead fish head protein is Coto Makassar seasoning had committed in the Chemistry Laboratory of Agro-industry Study Program, Pangkep State Agricultural Polytechnic, hydrolyzed snakehead fish head protein flour using the spray dryer drying method had brought about at the Center for Plantation Products in Makassar. The physicochemical analysis had done in the Chemical Laboratory, Department of Fisheries Product Processing Technology, Pangkep State Agricultural Polytechnic. Amino acid profile tests using the Ultra Performance Liquid Chromatography (UPLC) method were tested at the Saraswanti Indo Genetec Bogor laboratory. and analysis of volatile compounds had carried out at the Research Center for Flavor Analysis Laboratory of Rice Plants Sukamandi, Subang.
Methodology: The third research is the result of a study of Coto makassar seasoning flour products with the best protein to be applied to Coto Makassar seasoning flour. Applications made were snakehead fish head protein hydrolyzate and Coto seasoning flour treated with a ratio of 100% (Coto Seasoning Flour: HPKIG Flour) / (TC: THPKIG) was as follows (TC: THPKIG)1 = 90%: 10% (w/b) and (TC: THPKIG)2 = 80% : 20% (w/b). The best treatment result was carried out by the preference test on the protein coto seasoning produced, namely the study of the best ratio formula of 20 grams dissolved in boiling water A = 150 mL, B = 200 mL C = 250 mL.
Results: Characteristics of the application of 20% snakehead fish head protein hydrolyzate flour and 80% coto seasoning flour obtained a brightness value of L* 59.23%, hue 67.13%, moisture content 10.19%, ash content 11.48%, protein content 64.20%, 1.26% fat content and 3.35% albumin content. The highest amino acid is glutamic acid 20.68%. Sensory value of taste sample application of fish head protein hydrolyzate in coto Makassar seasoning 20% ​​with the addition of 200 mL of water Assessment criteria 8 (Very like) panelists prefer it because it feels the more spicy sensation
Conclusion: The result of the analysis obtained by the best treatment are the characteristics of the application of 20% hydrolyzed protein from snakehead fish head flour and 80% coto seasoning flour.
The Strategies of Chromite Terrace in Sukinda Valley, India: An Appraisal
Authors: Mishra Siba Prasad , Samal Arnada , Sohel Mohammed , Sethi Kumar Ch. , Patnaik Sanjeeb Kumar 
Published: January 2023

Iron chrome oxide (FeCr 2O4), is a commercially viable and major ingredient of stainless steel. The Odisha state in India possesses 98% of the pre-Cambrian India’s Chromite ore deposits in Sukinda valley, Jajpur District. To meet the present escalating demand for chromium in steel industries, it is urged to extract more chrome ore to satiate domestic needs. The depletion of chrome deposits, rise in demand, fewer chrome mines, and less conversion from tailings increase of more toxic hexavalent chrome ion level in the geo-bio hydrosphere, shall aggravate health concerns for the people, fauna, and flora in Sukinda Ultramafic Complex (SUC).
The present quest is a collection of chromite ores and tailings. A chemical study is done by using the X-ray fluorescent spectrometer. An insitu/GIS study of the Sukinda ultramafic complex by using Arc-GIS, and ERADAS software has been done to originate hydrology, aspect, and hill-shade map of the valley. The literature, and as an inhabitant of the area helped in preparing the strategic plan through Environmental Impact Assessment and Environmental Management Plan.
CR (III) is a dietary requirement. The anthropogenic activities and atmospheric exposure have converted Cr (III) to Cr (VI) in SUC and have surpassed the recommended values. The noxious Cr (VI) in the geo-bio-hydrosphere shall invite health and environmental concerns in the future. The aboriginals of SUC are economically burdened with food insecurity, poor livelihood, health, and of formal societal values. The Sukinda Valley ore samples contain 50% chromite ore is economic. But the >7% of CR (III) ore in the tailings and overburden shall warrant the future expected exorbitant Cr (VI) in the geo-bio-hydro environment of Sukinda valley.
Validation of the Computerized Suicide Risk Scale – a backpropagation neural network instrument (CSRS-BP)
Authors: Modai I. , Ritsner M. , Kurs R. , Mendel S. , Ponizovsky A. 
Published: July 2002

SummaryBackgroundMedically serious suicide attempts have been recognized as the most important predictor of suicide. The Computerized Suicide Risk Scale based on backpropagation neural networks (CSRS-BP) has been recently found efficient in the detection of records of patients who performed medically serious suicide attempts (MSSA).ObjectivesTo validate the CSRS-BP by: 1) using the CSRS-BP with patients instead of records; 2) comparing the ability of expert psychiatrists to detect MSSA, using the CSRS checklist; and 3) comparing the results of the Risk Estimator for Suicide (RES) and the self-rating Suicide Risk Scale (SRS) with the CSRS-BP.MethodsTwo hundred fifty psychiatric inpatients (35 MSSA and 215 non-MSSA) were diagnosed by clinicians using the SCID DSM-IV. Three expert psychiatrists completed the CSRS checklist, and the RES for each patient, and the patients completed the self-report SRS assessment scale. The CSRS-BP was run for each patient. Five other expert psychiatrists assessed the CSRS checklists and estimated the probability of MSSA for each patient. Comparisons of sensitivity and specificity rates between CSRS-BP, assessment scales and experts were done.ResultsInitially, the CSRS-BP, RES, SRS, and experts performed poorly. Although sensitivity and specificity rates significantly improved (two to four times) after the inclusion of information regarding the number of previous suicide attempts in the input data set, results still remained insignificant.ConclusionsThe CSRS-BP, which was very successful in the detection of MSSA patient records, failed to detect MSSA patients in face-to-face interviews. Information regarding previous suicide attempts is an important MSSA predictor, but remains insufficient for the detection of MSSA in individual patients. The detection rate of the SRS and RES scales was also poor and could therefore not identify MSSA patients or be used to validate the CSRS-BP.
Correlates of Attributing New Disability to Old Age
Authors: Sarkisian Catherine A. , Liu Honghu , Ensrud Kristine E. , Stone Katie L. , Mangione Carol M. , For The Study of  , Group Osteoporotic Fractures Research 
Published: July 2002

OBJECTIVES: To describe women who attribute new disability to old age and to identify demographic, medical, behavioral, and psychosocial characteristics that correlate with attributing new disability to old age.DESIGN: Prospective cohort study with 4‐year follow‐up.SETTING: Four geographic regions of the United States.PARTICIPANTS: 9704 women aged ≥67 years participating in the Study of Osteoporotic Fractures. Of these, 657 who reported no disability at baseline but at follow‐up reported difficulty carrying out 1 or more of 13 functional activities were eligible for our analysis.MEASUREMENTS: All women reporting difficulty in any functional activity at follow‐up were asked “What is the main condition that causes you to have difficulty or prevents you from (doing the activity)?” and were shown a card listing 14 medical conditions as well as the option “old age,” from which they could choose only one response. Women attributing difficulty or inability in 1 or more functional activities to old age were classified as attributing new disability to old age. We examined the relationship between attributing new disability to old age and the following characteristics measured at baseline: age, level of education, medical comorbidity, cognitive function, body mass index (BMI), gait speed, grip strength, visual acuity, physical activity level, smoking status, social network level, and depressed mood.RESULTS: Overall, 13.5% of women attributed new disability to old age. Age was a strong independent correlate of attributing new disability to old age: compared with women age 67 to 69, the odds of attributing new disability to old age for women age 70 to 79 was 3.6 times as large (95% confidence interval [CI] = 1.6–8.3), and for women age 80 or over was 5.5 times as large (95% CI = 2.1–14.7). The only other characteristic that remained an independent correlate of attributing new disability to old age was grip strength; for each decile decrease in grip strength, a woman's odds of attributing new disability to old age increased by 9% (odds ratio [OR] = 1.09, 95% CI = 1.01–1.19).CONCLUSIONS: Despite great advances in geriatric medicine, old age is still perceived as a causal agent in functional decline, especially among our oldest patients. Further study is needed to determine whether, how often, and under what circumstances older adults who attribute new disability to old age have medical conditions amenable to interventions that could preserve their functioning and improve their quality of life.
Clinical Features and Functional Outcome of Intracerebral Hemorrhage in Patients Aged 85 and Older
Authors: Arboix Adrià , Vall‐Llosera A. , García‐Eroles Lluis , Massons Joan , Oliveres Montserrat , Targa Cecilia 
Published: July 2002

OBJECTIVES:The importance of studies of older stroke victims is growing because of the changes in the age structure of Western populations. We determined demographic characteristics, clinical features, neuroimaging data, and outcome of acute spontaneous intracerebral hemorrhage occurring in people aged 85 and older.DESIGN:Prospective collection of data from a hospital‐based registry.SETTING:Sagrat Cor Hospital of Barcelona (an acute care, 350‐bed teaching hospital serving a population of approximately 250,000).PARTICIPANTS:Between January 1986 and December 1995, data were collected on 2,000 stroke patients admitted consecutively to the department of neurology (25 beds and an acute stroke unit).MEASUREMENTS:For the purpose of this study, all cases of intracerebral hemorrhage were selected (n = 229). Demographic data, clinical features, neuroimaging findings, and outcome variables (in‐hospital mortality and medical complications developed during hospitalization) in patients aged 85 and older (n = 28) were compared with patients who were younger than age 85 (n = 201). Distinctive clinical features of intracerebral hemorrhage in very old people were assessed by multivariate analysis.RESULTS:Intracerebral hemorrhage was diagnosed in 11% of subjects aged 85 and older included in the stroke registry and accounted for 12% of all cases of intracerebral hemorrhage. Very old people with intracerebral hemorrhage showed a significantly higher frequency of female gender (75% vs 32%, P < .005), altered consciousness (64% vs 43%, P < .05), multiple topographic involvement (29% vs 13%, P < .03), undetermined etiology of bleeding (50% vs 27%, P < .02), moderate or severe neurological deficit at hospital discharge (89% vs 58%, P < .005), and in‐hospital mortality (50% vs 27%, P < .01) than younger people. After multivariate analysis, female sex (odds ratio (OR) = 3.2, 95% confidence interval (CI) = 1.27–7.99) and moderate or severe neurological deficit at hospital discharge (OR = 4.75, 95% CI = 1.36–16.55) were independent clinical factors associated with intracerebral hemorrhage in very old people.CONCLUSIONS:Patients aged 85 and older with intracerebral hemorrhage showed some peculiar clinical features and poorer outcome, including higher in‐hospital mortality and moderate or severe neurological deficit at hospital discharge, than younger patients with intracerebral hemorrhage. J Am Geriatr Soc 50:449–454, 2002.
Mitochondrial Proliferation and Paradoxical Membrane Depolarization during Terminal Differentiation and Apoptosis in a Human Colon Carcinoma Cell Line
Authors: Mancini Mariangela , Anderson Benjamin O. , Caldwell Elizabeth , Sedghinasab Monireh , Paty Philip B. , Hockenbery David M. 
Published: July 2002

Herbimycin A, a tyrosine kinase inhibitor, induces cellular differentiation and delayed apoptosis in Colo-205 cells, a poorly differentiated human colon carcinoma cell line. Cell cycle analysis in conjunction with end labeling of DNA fragments revealed that G2 arrest preceded apoptotic cell death. Ultrastructural examination of herbimycin-treated cells demonstrated morphologic features of epithelial differentiation, including formation of a microvillar apical membrane and lateral desmosome adhesions. A marked accumulation of mitochondria was also observed. Fluorometric analysis using the mitochondrial probes nonyl-acridine orange and JC-1 confirmed a progressive increase in mitochondrial mass. However these cells also demonstrated a progressive decline in unit mitochondrial transmembrane potential (ΔΨm) as determined by the ΔΨm-sensitive fluorescent probes rhodamine 123 and JC-1 analyzed for red fluorescence. In concert with these mitochondrial changes, Colo-205 cells treated with herbimycin A produced increased levels of reactive oxygen species as evidenced by oxidation of both dichlorodihydrofluorescein diacetate and dihydroethidium. Cell-free assays for apoptosis using rat-liver nuclei and extracts of Colo-205 cells at 24 h showed that apoptotic activity of Colo-205 lysates requires the early action of mitochondria. Morphological and functional mitochondrial changes were observed at early time points, preceding cleavage of poly (ADP-ribose) polymerase.
These results suggest that apoptosis in differentiated Colo-205 cells involves unrestrained mitochondrial proliferation and progressive membrane dysfunction, a novel mechanism in apoptosis.
On the Brylinski-Kostant filtration
Authors: Joseph Anthony , Letzter Gail , Zelikson Shmuel 
Published: July 2002

Let

g

\mathfrak g

be a semisimple Lie algebra and

V
V

a finite dimensional simple

g

\mathfrak g

module. The Brylinski-Kostant (simply, BK) filtration on weight spaces of

V
V

is defined by applying powers of a principle nilpotent element. It leads to a

q
q

-character of

V
V

. Through a result of B. Kostant the BK filtration of the zero weight space is determined by the so-called generalized exponents of

g

\mathfrak g

. Later R. K. Brylinski calculated the BK filtration on dominant weights of

V
V

assuming a vanishing result for cohomology later established by B. Broer. The result could be expressed in terms of

q
q

polynomials introduced by G. Lusztig. In the present work, Verma module maps are used to determine the BK filtration for all weights. To do this several filtrations are introduced and compared, a key point being the graded injectivity of the ring of differential operators on the open Bruhat cell viewed as a

g

\mathfrak g

module under diagonal action. This replaces cohomological vanishing and thereby Brylinski’s result is given a new proof. The calculation for non-dominant weights uses the fact that the corresponding graded ring is a domain as well as a positivity result of G. Lusztig which ensures that there are no accidental cancellations. This method allows one to compare the BK filtrations in adjacent chambers.
Automated genome sequence analysis and annotation.
Authors: Andrade M A , Brown N P , Leroy C , Hoersch S , de Daruvar A , Reich C , Franchini A , Tamames J , Valencia A , Ouzounis C , Sander C 
Published: July 2002

Abstract
MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit
CpGProD: identifying CpG islands associated with transcription
start sites in large genomic mammalian sequences
Authors: Ponger Loı̈c , Mouchiroud Dominique 
Published: July 2002

Abstract
Results: CpGProD is an application for identifying mammalian promoter regions associated with CpG islands in large genomic sequences. Although it is strictly dedicated to this particular promoter class corresponding to ≈50% of the genes, CpGProD exhibits a higher sensitivity and specificity than other tools used for promoter prediction. Notably, CpGProD uses different parameters according to species (human, mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand.
Availability: http://pbil.univ-lyon1.fr/software/cpgprod.html
Supplementary information: http://pbil.univ-lyon1.fr/software/cpgprod.html
Contact: ponger@biomserv.univ-lyon1.fr
* To whom correspondence should be addressed.