Miracle-dz/UniFAR-FTUs huggingface dataset:
METHODS DEVELOPMENT IN BIOLOGICAL MASS SPECTROMETRY: APPLICATION IN GLYCOPROTEOMICS

METHODS DEVELOPMENT IN BIOLOGICAL MASS SPECTROMETRY: APPLICATION IN GLYCOPROTEOMICS Proteomics refers to global characterization of the full set of proteins present in a biological sample. Various analytical disciplines contribute to proteomics but mass spectrometry became method of choice for analysis of complex protein samples. Mass spectrometry allows for high throughput analysis of the proteome but, moreover, it has the ability to acquire higher-order information such as post-translational modifications (PTM). Glycosylation is the most abundant PTM on eukaryotic proteins. This dissertation will focus on method development for structural proteomics that will be utilized to explain the glycoproteome of obligate intracellular protozoan parasite Toxoplasma gondii as a model system. Optimization of sample preparation is addressed in the first part of this dissertation. Sample preparation for mass spectrometry analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation significantly impacts the separation and identification capabilities of mass spectrometers. Also, there are problems unique to intracellular parasites as limited amount, host cell impurity and choice of the host. The additional obstacle is to extract only glycosylated proteins for which there is no one standard method. Here we report the optimal sample preparation method utilizing agarose bound Concanavalin A (Con A) beads to efficiently pull down glycoproteins, dialyze and analyze them using MuDPIT. This method was further enhanced by passing the non-retained protein fraction (first flow-through) through a second Con A column and then passing the second non-retained protein fraction (second flow-through) through the third Con A column (3 sequential pull-downs) yielding 394 benchmark proteins. Glycoproteome of Toxoplasma gondii is not yet fully understood. However, evidence suggests that glycosylation could be essential for cyst formation and maintenance which is characteristic of chronic stage of disease. The focus of the second part of dissertation is to better understand the differences in glycoproteomes of tachizoites and tissue cysts. Cyst proteins pulled down using optimized sample preparation method that do not appear in the tachyzoites pulldowns could be critical elements in the structural stability of the tissue cyst.
Pengembangan E-Book Fisika Berbasis Multi Representasi dengan Corrective Feedback pada Materi Gerak Lurus Kelas X SMA/MA

Penelitian ini bertujuan untuk mengembangkan dan mengatahui kelayakan e-book fisika berbasis multi representasi dengan corrective feedback pada materi gerak lurus kelas X SMA. Penelitian ini mengadaptasi model penelitian dan pengembangan Four-D , namun hanya dilaksanakan sampai tahap ketiga yaitu uji coba terbatas. E-book yang dihasilkan berupa aplikasi berbasis web yang menyajikan konsep dalam berbagai representasi dan dilengkapi latihan soal multi representasi dengan corrective feedback . Berdasarkan hasil penelitian menunjukkan bahwa e-book yang telah dikembangkan memperoleh kriteria valid dengan nilai rata-rata validasi materi 3,90 dan validasi media 3,86. Dari uji kepraktisan produk memperoleh kriteria praktis dengan persentase 97,3%. Dengan demikian produk tersebut telah berhasil dikembangkan dan layak digunakan oleh siswa.
Ectomycorrhizal Formation In Vitro of Pinus elliottii and Pinusarmandii with Tricholoma matsutake Isolates fromSouthwestern China

Tricholoma matsutake is an edible ectomycorrhizal mushroom (ECM) with high ecological and economic value. The mycorrhizal synthesis in vitro with T. matsutake isolates from Japan and Finland has been investigated in detail and widely reported. However, up to now there is no detailed description of morphological and anatomical characteristics of synthesized mycorrhizae in vitro with T. matsutake isolates from China under controlled laboratory conditions. In this study, using pure-culture ager plate systems, we demonstrated that a T. matsutake isolate from Southwestern China could form well-developed ectomycorrhiza with both exotic tree Pinus elliottii and indigenous tree Pinus armandii. The mycorrhizal association included fungal mantle sheaths and well-developed Hartig nets. P. elliottii is widely planted in the world, and it has important economic value in the timber and resin industries, whereas P. armandii is native to China and popularly planted in the central and southwestern China. Interestingly, the formation of mycorrhizae of P. elliottii was earlier and more abundant compared with P. armandii in the pureculture plate system. Our findings provide a new perspective to study the cultivation of T. matsutake in the world, and also to the propagation of the mycorrhizal P. elliottii and P. armandii seedlings in China.
Impact inoculum dosage of lactic acid bacteria on oat and wheat silage fermentation at ambient and low temperatures

Abstract. Lactic acid bacteria (LAB) can be used as silage additives to ensure rapid and vigorous fermentation at early stages of ensiling. We predicted that the optimal LAB inoculation dosage for forage at ambient temperature (15–38°C) would be different from that at cold temperature (4°C). In this study, Lactobacillus plantarum QZ227, isolated from a wheat landrace in alpine regions of Qinghai, China, and commercial L. plantarum FG1 were used as inoculum, with sterile water as control. The effects of inoculum dosage on the fermentation quality of oat (Avena sativa L. cv. Qinghai) and wheat (Triticum aestivum L. cv. Yumai No. 1) silage at ambient temperature (15–38°C) and at 4°C were investigated in laboratory experiments. Little or no improvement in silage quality occurred upon increasing the inoculum dosage at ambient temperature. By contrast, a lower pH and NH3-N content, and a higher LAB count and lactic acid content, were observed at 4°C. Furthermore, the growth of Escherichia coli was inhibited effectively at the lower temperature, and silage quality was positively correlated with increasing inoculum dosage (P < 0.05). These results suggest that increasing the inoculum dosage could improve the quality of silage at lower temperatures of 4°C, whereas an appropriate dosage was a key factor for silage at ambient temperature. In this study, oat forage could be used as raw materials for ensiling only at low temperature but was not suitable for ensiling at ambient temperature without wilting due to the high moisture content (86.55%). QZ227 isolated from the roots of wheat in alpine regions displayed superior antimicrobial properties against yeast at ambient temperature and E. coli at 4°C compared with commercial strain FG1. This is the first study to explore the effects of inoculum dosage on silage quality at low temperatures, and provides a basis for low-temperature silage technologies.
From gene to disorder in ADHD: Mapping mechanisms at different levels of complexity

Attention-Deficit/Hyperactivity Disorder (ADHD), is a common neurodevelopmental disorder. While ADHD is diagnosed at the behavioral level, it is a neurobiological disorder that is most likely caused by a complex interplay between genetic and environmental risk factors. Despite its high heritability, gene identification has been challenging in ADHD. The aim of this thesis was (1) to discover genetic variants that contribute to the development of this disorder and (2) to identify the underlying (neuro)biological mechanisms. Understanding which genetic variants are relevant for the disorder can yield insights into the pathophysiology and potentially (in the long run) lead to novel treatment options. By applying various statistical genetics approaches, such as genome-wide association studies on common genetic variants or by combining linkage analyses with whole-exome sequencing in multigenerational families, we identified individual novel genetic risk factors for ADHD. Additionally, we obtained insights into the global genetic architecture of ADHD. The second part of the thesis focused on different approaches that can help to map the biological mechanisms from gene to the disorder. Neurobiological parameters, such as behavioral outcomes and brain volume measurements, were used both in animal models and in humans to link genetic variation to ADHD symptomatology. In ADHD, most brain imaging genetics studies focused on the investigation of single genetic variants. Among other findings, we were able to show that ADHD and the intracranial volume are significantly negatively correlated at the global genetic level, resembling earlier phenotypic observations.
Mechanism of SPS acceleration in a PEG containing copper plating bath

Deposition of copper in Through Silicon Vias (TSVs) is achieved by addition of organic compounds, which act as suppressors and accelerants to copper electroplating solutions. The focus of this study is on the acceleration effect of bis-(3-sodiumsulfopropyl) disulfide (SPS) which is believed to go through an electrochemical reaction to form sodium 3-mercapto-1-propanesulfonate (MPS), the effective accelerant. The accelerant is believed to operate by forcing the suppressor off the copper surface through competitive adsorption. The kinetics of MPS adsorption onto copper was studied by addition of MPS to solutions containing the suppressor molecule, polyethylene glycol (PEG), under constant overpotential and measurement of the resulting current increase. The electrochemical cleavage of SPS to form MPS was also studied. SPS was placed in an acid solution in the absence of cupric ions and an overpotential was applied to split the molecule. A new method for measuring MPS concentration was developed and used to determine the amount of MPS generated. An improved model for the acceleration effect of SPS on copper deposition was developed. First SPS diffuses to the metal surface at a rate that can be quantified by Fick's laws of diffusion. When the molecule reaches the electrode, it splits at the sulfur-sulfur bond in a reaction which is electrochemically driven. Higher overpotentials drive faster reaction rates. The resulting molecule adsorbs rapidly enough that coverage of the surface can be considered to be completely mass transfer controlled. The area covered by one MPS molecule on the saturated metal surface was determined to be 47 +/9 A2. This value is higher than would be expected only considering steric hindrance which suggests that repulsion between negatively charged sulfonate ends contributes to the spacing.
Spatial Organization and Social Dynamics of Geoffroy's Cat in the Brazilian Pampas

Geoffroy's cat (Leopardus geoffroyi) is a small Neotropical felid whose social behavior remains poorly understood. We used simultaneous radiotelemetry (4 males and 3 females) and camera trapping to examine the spatial structure and dynamics of a population of this species in the Brazilian pampas (part of the Uruguayan Savannah ecoregion), including assessment of interindividual genetic relatedness. Home ranges (HRs) and core areas of males were larger than those of females. Males were significantly heavier than females, and linear regression analyses indicated that body mass of males significantly influenced HR size, whereas the relationship was not significant for females. When we performed a joint analysis comparing our data to those reported previously for other study sites, we observed the same patterns. We detected extensive HR and core area overlap among most of our monitored individuals, with no clear sex-based pattern. Moreover, our molecular data indicated that most of the sampled individuals were unrelated, and that the levels of HR and core area overlap were not significantly influenced by genetic relatedness. These results suggest that some interindividual tolerance and relaxation in territoriality may occur in Geoffroy's cat. We detected only minor changes in HR and core area size and overlap between seasons, indicating that the spatial structure we observed was temporally stable. On a broader perspective, our cross-site comparisons illustrate the usefulness of performing multiple ecological studies employing comparable methods at different locations to better understand the ecology of wild felid populations.
A pilot study of a novel molecular host response assay to diagnose infection in patients after high-risk gastro-intestinal surgery

Aim SeptiCyte LAB measures the expression of four host-response RNAs in blood to distinguish sepsis from sterile inflammation. Sequential monitoring of this assay may have diagnostic utility in patients at high risk for postoperative infectious complications. Methods In this pilot study we studied esophagectomy patients who had developed a complication within 30 days following surgery as well as a random sample of 100 uncomplicated postoperative patients. PAXgene blood samples were collected postoperatively and whenever a complication occurred. SeptiCyte scores (ranging 0-10 with increasing likelihood of infection) were compared to post-hoc physician adjudication of infection likelihood using strict definitions. Results Among 370 esophagectomy patients, 120 (32%) subjects developed a complication requiring ICU (re)admission, 63 (53%) of whom could be analyzed. Immediate postoperative SeptiCyte LAB scores were highly variable, yet similar for patients having a complicated and uncomplicated postoperative course (median score of 2.4 (IQR 1.6-3.3) versus 2.2 (IQR 1.3-3), respectively). Scores increased as complications developed, but this rise was higher for 34 subjects having confirmed infection (median difference 4.7 (IQR 4.1-5.8)) then for 12 subjects with a non-infectious complication (2.1 (IQR 0.4-3.6); p<0.0001). When 17 cases with undetermined infectious status were excluded, addition of SeptiCyte LAB to CRP resulted in improved diagnostic discrimination (AUC 0.88 (95%CI 0.77-0.99)) compared to CRP alone (AUC 0.76 (95%CI 0.61-0.91); p=0.04). Conclusions Sequential measurement of SeptiCyte LAB may have clinical utility in surgical patients at high risk of postoperative infection, but its diagnostic performance in this setting needs to be further evaluated.
A community-based randomized trial for the prevention and control of brucellosis among rural populations in Iran: application of the PRECEDE planning model

Background: Brucellosis is one of the most frequently occurring zoonotic diseases of veterinary and a public health problem in developing countries. It affects human and animal health and has measurable effects on the productive and reproductive performance of livestock. Therefore, the main purpose of this study was to develop a community-based intervention program for brucellosis prevention and control. A two-arm parallel cluster randomized controlled trial investigated the effectiveness of the program over six months in a rural population in Ahar, East Azerbaijan, Iran. A total of 16 village health houses were randomly allocated to the intervention and the control groups (eight per arm), and 400 participants were recruited via household health records in the health houses. The PRECEDE model, which is an acronym for Predisposing, Reinforcing and Enabling Constructs in Educational Diagnosis and Evaluation, was used to design, implement, and evaluate the brucellosis prevention and control program. Knowledge, attitudes, self-efficacy, social support, environmental enabling, and behavioral factors were measured at the baseline and the six-month follow-up. A generalized mixed effects model was used to analyze data. Results: The mean ages (SD) of the intervention and control group respondents were 35.9 (11.87) and 37.28 (11.04) years, respectively. After the six-month intervention, significant between-group differences were found on all PRECEDE variables, adjusted for education, history of brucellosis, and family history of brucellosis. Conclusion: There is a need to consolidate collaborative health and veterinary sector efforts, as well as increase regular vaccination practices and financial resources to support farmers willing to slaughter animals and/or offer slaughter facilities. The present study was able to demonstrate which educational and ecological factors influence behaviors and environments related to brucellosis and, as such, provide evidence of the effectiveness of interventions based on the PROCEDE model.
Anxiety and Depression Symptoms Among Ovarian Cancer Patients in Western China: A Cross-Sectional Study

It is well known that cancer patients tend to have different degrees of depression and anxiety. However, there are few studies focus on the association between symptoms of depression and anxiety among ovarian cancer patients and their coping styles in western China. In this study, we aim to investigate the prevalence of cancer-related depression and anxiety in western China among patients with ovarian cancer, and analyze their influencing factors, to provide clinical guides for psychological interventions.
Knowledge and Attitude toward Human Papillomavirus Infection and Vaccination among Thai Women: A Nationwide Social Media Survey

Objectives: This study was performed first to assess Thai women’s knowledge and attitude toward Human papillomavirus (HPV) infection and vaccination and second to find out factors associated with knowledge in this regard. Methods: The survey announcement was advertised via Facebook from 17 May 2019 to 14 June 2019 to recruit women aged 18-26 years living in Thailand. A score below 5 out of total score of 10 on the survey was considered as a poor level of knowledge. Multivariate analysis was applied to identify factors associated with HPV infection and vaccination knowledge. Results: A total of 1,175 participants were recruited. The participants’ median age was 22 years. Approximately, 46% of the participants had poor level of knowledge regarding HPV infection and vaccination. Factors associated with poor knowledge included low educational level (adjusted OR, 1.35; 95% CI 1.04-1.77), low family income (adjusted OR, 2.14; 95% CI 1.65-2.78), being Christian (adjusted OR, 4.04; 95% CI 1.22-13.40), being engaged in sexual intercourse (adjusted OR, 0.75; 95%CI 0.58-0.97), and being unvaccinated against HPV infection (adjusted OR, 5.74; 95% CI 3.07-10.74). Conclusion: Nearly half of the Thai women who participated in the survey had poor level of knowledge regarding HPV infection and vaccination, indicating a need for more effective health education intervention. Factors associated with knowledge included socioeconomic status and sexual behavior.
Dental Fluorosis: Dilemma of Genetic Susceptibility

Excessive exposure to fluoride during formation of teeth may lead to a severe hypomineralization condition, called dental fluorosis. Genes such as Collagen type 1 alpha 2 (COL1A2), Estrogen receptor (ESR), Prolactin (PRL), Catechol-o-methyltransferase (COMT), matrix metalloproteinase 20 (MMP20) and many others have been implicated in the incidence of dental fluorosis. This mini-review is an insight into the fact that fluorosis incidence and intensity are significantly related to individual’s genetic background.
First Report of the Occurrence of Oithona davisae Ferrari F.D.&Orsi, 1984 (Copepoda: Oithonidae) in the Southern Black Sea, Turkey

We report the first occurrence of Oithona davisae Ferrari F.D. &Orsi, 1984 in the Sinop coast, Turkey. Data on the abundance and biomass of this species, and the proportion of adult and copepodite stages in the total copepods were investigated. The zooplankton samples were collected monthly by vertical hauls with plankton net of 112 μm mesh size from January to December 2009. However, O. davisae was observed for the first time in September, and continued to be observed for the remainder of the sampling period. The highest abundance and biomass of this species were recorded in November 2009 (1485.35 ind.m and 2.9 mg.m, respectively), which was 39.89% in the abundance and 14.35% of the biomass of the total copepods in November. In conclusion, the non-indigenous copepod species, O. davisae, has adapted to the ecological conditions of the Sinop coast.
Influence of soil contamination before and after ensiling on mineral composition of grass silages, feed intake and carry-over to body tissue of goats

Iron (Fe) is ubiquitous in the environment and has possible impact on quality and safety of feed and food due to the fact that it can be transferred from soil to animal feed and further to the products of animal origin. Therefore, the objective of the present study was to evaluate the effect of contamination of forage with soil differing in Fe concentration on Fe solubility, mineral composition and quality of grass silages. Furthermore, the effect of feeding these silages on feed intake, performance, trace element absorbability and carry-over into edible tissues was tested in young goats. Two ensiling experiments revealed that treating grass without or with different levels and types of soil before ensiling did not affect fermentation parameters of silages. Nevertheless, the addition of soil caused a highly significant increase of crude ash and trace elements contents in forage and silages. During ensiling, the in vitro solubility of Fe increased on average 5 times. Also, the aluminium content was the best indicator of soil contamination in forages. In a feeding trial with growing goats, feed intake and live weight gain were decreased in the group fed grass ensiled with the soil in contrast to the control group and animals receiving feed with soil added just before feeding. Fe concentration was highest in the duodenal tissue of kids fed the forage contaminated with soil before ensiling (184 vs 88-80 mg Fe/kg DM in the other two treatments), which might be also an indicator of Fe regulating properties. Fe concentration in the liver increased likewise. In conclusion, data indicate that ingesting ensiled soil impairs animal performance.
Body Size Increases with Elevation in Pyrenean Newts (Calotriton asper)

Abstract: Phenotypic variation along environmental gradients—particularly in body size—occurs in a variety of species. Larger-bodied individuals are usually found in colder climates, as predicted by Bergmann's rule. In ectotherms, this pattern remains controversial. Among thermoconformers, smaller body sizes are expected in colder climates because these species might have relatively shorter warm-up times (advantageous in cold climates), whereas the reverse pattern can be expected in thermoregulators (heat-balance hypothesis). In amphibians, additional factors like humidity and thermal niche might also contribute to body-size variation. Following Allen's rule, there can also be a negative relationship between temperature and relative limb length. Here, we described associations among temperature, precipitation, body size, and relative limb length in Calotriton asper. We expected individuals from higher elevations (colder climates) to be smaller when compared to lowelevation conspecifics. We found an influence of temperature on body-size variation but, contrary to expectations, salamanders from colder climates were larger compared to low-elevation populations, which corroborates with the heat-balance hypothesis. In accordance with the converse water-availability hypothesis, we also demonstrated that precipitation was related to body-size variation in this species. Finally, our results supported the predictions of Allen's rule. This trend could be the result of evolutionary responses to harsh environments, driven by either local adaptation, plasticity processes, or a combination of both.