Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes of soil bioavailable phosphorus content in the long-term field fertilizing experiment

The aim of this study is to describe the changes of bioavailable phosphorus content in soil in long-term 18 years field experiments with different fertilizing systems. The field experiments are located at three sites with different soil and climatic conditions in the Czech Republic (Červený Újezd, Humpolec and Prague-Suchdol). Same fertilizing systems and crop rotation (potatoes (maize) – winter wheat – spring barley) are realized at each site with following fertilizing treatments: (1) unfertilized treatment (control), (2) farmyard manure (FYM), (3) and (4) sewage sludge (SS 1 and SS 3), (5) mineral nitrogen (N), (6) mineral nitrogen with straw (N + straw) and (7) mineral nitrogen with phosphorus and potassium (NPK). The long-term fertilizing effect on available P content changes in soil was observed. Bioavailable phosphorus content in soil increased in treatments with organic fertilization after 18 year experiment at all sites. The treatments SS 3 had the highest increase at all sites. The highest bioavailable P content increase compared to control (258 mg/kg) was determined at site Červený Újezd. On the contrary, available phosphorus content decreased at treatments with mineral fertilization and control treatment among all sites. Bioavailable P content decrease in the treatment NPK was observed, although phosphorus was applied. The lowest differences in available P content among all fertilizing treatments were observed at the location Prague-Suchdol.
Evaluation of MicroScan rapid panels for detection of high-level aminoglycoside resistance in enterococci

The ability of MicroScan rapid panels to detect high-level aminoglycoside-resistant enterococci was evaluated. By agar dilution, 46 of 139 isolates were susceptible to gentamicin (GNT) and streptomycin (STRP); the rest were highly resistant to one or both agents. Rapid panels detected 97.5% of STRP- and GNT-resistant isolates and had a specificity of 95.6%. Detection of resistance by conventional panels at 18 h was 64.6% for STRP and 90.2% for GNT.
Vertebroplasty--high viscosity cement versus low viscosity cement.

The patients with intensive pain caused by the vertebra body fracture were treated by application of low viscosity cement (LVC), (Vertebroplastic, DePuy) and high viscosity cement (HVC), (Confidence, DePuy,) into the body, by means of diascopy through unilateral transpendicular approach. Application of LVC was made in 75 patients, on 109 vertebrae, and HVC was applied in 12 patients on 14 vertebrae. Application of LVC was performed on 48 thoracic and 61 lumbar vertebrae and 5 thoracic and 9 lumbar vertebrae were stabilized with HVC. 43 patients were treated for malignancy and in 38 for osteoporosis. For LVC, preoperative VAS score was 8.32 and 2.23 (p < 0.00001) 24 hours after surgery, and it remained stable 3 month later. For HVC, preoperative VAS score was 7.99 and it was 2.5 (p < 0.00001) 24 hours after surgery and 3 months later. In the group of patients treated with LVC, there was 1 serious complication, a paraparesis caused by the leakage of cement into the spinal canal, which was partially recovered after decompression and rehabilitation treatment and 2 superificial infections with S. epidermidis which were cured by means of antibiotics. In 32 vertebrae (32) cement leakage extra ossal, either into vein plexus or intradiscal during surgery were noticed. When HVC was applied, intradiscal leakage occurred in one case only (8%). By means od Wilcoxon paired test a significant difference was found between the preoperative VAS, and the values immediately after surgery and 3 months later (Z = 7.52, p < 0.00001) when LVC was applied. , and with HVC it was ( Z = 3.04, p < 0.00001), which indicates that the fast achieved pain reduction remained stable during the 3 month follow-up. The vertebroplasty is a safe and efficient surgical method in treatment of compressive vertebrae fractures which do not react to the conventional method of treatment. This method, when HVC is applied, shows significantly less complications related to cement leakage.
Inhibition of in vitro and in vivo brown fat differentiation program by myostatin

Objective: Obesity arises mainly due to the imbalance between energy storage and its expenditure. Metabolically active brown adipose tissue (BAT) has recently been detected in humans and has been proposed as a new target for anti‐obesity therapy because of its unique capacity to regulate energy expenditure. Myostatin (Mst), a negative regulator of muscle mass, has been identified as a potential target to regulate overall body composition. Although the beneficial effects of Mst inhibition on muscle mass are well known, its role in the regulation of lipid metabolism, and energy expenditure is not very clear.
Randomized controlled trial assessing the efficacy of a reusable fish-shaped iron ingot to increase hemoglobin concentration in anemic, rural Cambodian women.

Background: Anemia affects 45% of women of childbearing age in Cambodia. Iron supplementation is recommended in populations in which anemia prevalence is high. However, there are issues of cost, distribution, and adherence. A potential alternative is a reusable fish-shaped iron ingot, which, when added to the cooking pot, leaches iron into the fluid in which it is prepared.Objective: We sought to determine whether there was a difference in hemoglobin concentrations in rural Cambodian anemic women (aged 18-49 y) who cooked with the iron ingot or consumed a daily iron supplement compared with a control after 1 y.Design: In Preah Vihear, 340 women with mild or moderate anemia were randomly assigned to 1) an iron-ingot group, 2) an iron-supplement (18 mg/d) group, or 3) a nonplacebo control group. A venous blood sample was taken at baseline and at 6 and 12 mo. Blood was analyzed for hemoglobin, serum ferritin, and serum transferrin receptor. Hemoglobin electrophoresis was used to detect structural hemoglobin variants.Results: Anemia prevalence was 44% with the use of a portable hemoglobinometer during screening. At baseline, prevalence of iron deficiency was 9% on the basis of a low serum ferritin concentration. There was no significant difference in mean hemoglobin concentrations between the iron-ingot group (115 g/L; 95% CI: 113, 118 g/L; P = 0.850) or iron-supplement group (115 g/L; 95% CI: 113, 117 g/L; P = 0.998) compared with the control group (115 g/L; 95% CI: 113, 117 g/L) at 12 mo. Serum ferritin was significantly higher in the iron-supplement group (73 μg/L; 95% CI: 64, 82 μg/L; P = 0.002) than in the control group at 6 mo; however, this significance was not maintained at 12 mo (73 μg/L; 95% CI: 58, 91 μg/L; P = 0.176). Conclusions: Neither the iron ingot nor iron supplements increased hemoglobin concentrations in this population at 6 or 12 mo. We do not recommend the use of the fish-shaped iron ingot in Cambodia or in countries where the prevalence of iron deficiency is low and genetic hemoglobin disorders are high. This trial was registered at clinicaltrials.gov as NCT02341586.
BAC clones related to prognosis in patients with esophageal squamous carcinoma: an array comparative genomic hybridization study.

PURPOSE The prognosis of patients with esophageal carcinoma is poor. To identify genomic alterations associated with poor patient prognosis, we analyzed whole DNA copy number profiles of esophageal squamous carcinomas (ESCs) using array-based comparative genomic hybridization (aCGH). MATERIALS AND METHODS Twenty-one operated and two biopsied cases of esophageal squamous cancer were examined for study. Each sample was laser microdissected to obtain pure cancer cell populations. The extracted DNA was analyzed using aCGH. RESULTS One of the most representative alterations was a previously reported amplification at 11q13.3. In addition, some novel alterations, such as deletion of 16p13.3, were identified. Of the 19 patients who were reassessed more than 5 years after the operation, nine were still living and 10 had died from disease recurrence. When aCGH profiles from the surviving group and the deceased group were compared, significant differences were recognized in 68 of 4,030 bacterial artificial chromosome (BAC) clones. Almost half of these clones were present at nine limiting regions in 4q, 13q, 20q, and Xq. For 22 of these 68 BAC clones, there also was a significant difference in the Kaplan-Meier survival curve, using the log-rank test, when comparing patients who had an alteration in a particular clone with those who did not. CONCLUSIONS aCGH study of esophageal squamous cancer clearly identified BAC clones that are related to the prognosis of patients. These clones give us the opportunity to determine specific genes that are associated with cancer progression.
Connectivity Changes Underlying Neurofeedback Training of Visual Cortex Activity

Neurofeedback based on real-time functional magnetic resonance imaging (fMRI) is a new approach that allows training of voluntary control over regionally specific brain activity. However, the neural basis of successful neurofeedback learning remains poorly understood. Here, we assessed changes in effective brain connectivity associated with neurofeedback training of visual cortex activity. Using dynamic causal modeling (DCM), we found that training participants to increase visual cortex activity was associated with increased effective connectivity between the visual cortex and the superior parietal lobe. Specifically, participants who learned to control activity in their visual cortex showed increased top-down control of the superior parietal lobe over the visual cortex, and at the same time reduced bottom-up processing. These results are consistent with efficient employment of top-down visual attention and imagery, which were the cognitive strategies used by participants to increase their visual cortex activity.
Comparison of age-related changes in anti-Müllerian hormone levels and other ovarian reserve tests between healthy fertile and infertile population

Abstract In this study, we aimed to determine whether anti-Müllerian hormone (AMH) levels vary between fertile and infertile populations and compare them with basal follicle-stimulating hormone (FSH) levels and antral follicle count (AFC). This was a prospective study that included 177 primarily infertile patients who underwent IVF treatment and 162 healthy fertile patients admitted to our clinic for benign diseases. FSH and AMH levels and the AFC of the infertile and fertile populations were compared between the age categories <30, 30–39 and ≥40. Correlations between AMH, basal FSH, and AFC with age were evaluated. AFC and AMH levels did not differ between the fertile and infertile groups in all age categories. AMH was inversely correlated with age in both the fertile and infertile populations. However, AFC revealed a stronger correlation with age in both the fertile and infertile populations compared with basal FSH and AMH. Age was positively correlated with basal FSH and inversely correlated with AMH and AFC. In conclusion, there was no significant difference between the fertile and infertile populations in terms of AMH or AFC. The decrease in ovarian reserve in infertile patients is directly related to age, not infertility.
Risk stratification based on the clinical factors at diagnosis is closely related to the survival of localized osteosarcoma

Survival of osteosarcoma patients has reached a plateau with the addition of chemotherapy and in part predicted based on histologic response. Risk‐adapted therapy might be an alternative approach. We aimed to identify risk groups using clinical variables available at time of diagnosis in order to better predict outcomes and form the basis for risk‐adapted therapy.
Named Entity Recognition of Persons’ Names in Arabic Tweets

The rise in Arabic usage within various social media platforms, and notably in Twitter, has led to a growing interest in building Arabic Natural Language Processing (NLP) applications capable of dealing with informal colloquial Arabic, as it is the most commonly used form of Arabic in social media. The unique characteristics of the Arabic language make the extraction of Arabic named entities a challenging task, to which, the nature of tweets adds new dimensions. The majority of previous research done on Arabic NER focused on extracting entities from the formal language, namely Modern Standard Arabic (MSA). However, the unstructured nature of the colloquial language used in tweets degrades the performance of NER systems developed to support formal MSA text. In this paper, we focus on the task of Arabic persons‟ names recognition. Specifically, we introduce an approach to extract Arabic persons‟ names from tweets without employing any morphological analysis or languagedependent features. The proposed approach adopts a rule-based model combined with a statistical one. This approach uses unsupervised learning of patterns and clustered dictionaries as constrains to identify a person‟s name and resolve its ambiguity. Our approach outperforms the best reported result in the literature on the same test set by an increase of 19.6% in the F-score.
The suburbanisation process in a depopulation context in the Katowice conurbation, Poland

Abstract The Katowice conurbation is an example of a typical old industrial region in Central and Eastern Europe, whose socioeconomic transformation, initiated after 1990, has led to spatial and functional changes. The aim of this article is to present the suburbanisation process in the Katowice conurbation based on demographic changes and an analysis of migration flow. This process has been taking place in the area since the 2000s and takes on the shape of a multi-centre development of newly created individual and developed housing zones (both in the core and in the suburban area of the conurbation). Since 1990, the cities of the Katowice conurbation have been undergoing a process of shrinking. This process is manifested in the decline in number of urban residents in the years 1991–2016, amounting to 366 thousand people. Moreover, the cities face numerous social, economic and spatial problems. Since 1995, simultaneous with the shrinking of the cities of the Katowice conurbation, there has been an increase in the number of inhabitants in its suburban areas (since 2004, the trend has continued to be positive). Population increases have also been recorded in some inner-city zones of the conurbation. The suburbanisation process in the outer zone of the conurbation includes, in particular, the communes located north and south of the cities constituting its core, including the communes of Ożarowice, Psary, Mierzęcice in the north and Mikołów, Orzesze, Wyry in the south-west. On the other hand, the areas of intense inner-city construction development, located in the areas of the Katowice conurbation core, which are attractive in terms of environment and transportation, are undergoing so-called, “internal suburbanisation”.
Supporting adaptable granularity of changes for massive-scale collaborative editing

Since the Web 2.0 era, the Internet is a huge content editing place in which users contribute to the content they browse. Users do not just edit the content but they collaborate on this content. Such shared content can be edited by thousands of people. However, current consistency maintenance algorithms seem not to be adapted to massive collaborative updating. Shared data is usually fragmented into smaller atomic elements that can only be added or removed. Coarse-grained data leads to the possibility of conflicting updates while fine-grained data requires more metadata. In this paper we offer a solution for handling an adaptable granularity for shared data that overcomes the limitations of fixed-grained data approaches. Our approach defines data at a coarse granularity when it is created and refines its granularity only for facing possible conflicting updates on this data. We exhibit three implementations of our algorithm and compare their performances with other algorithms in various scenarios.
Optimising post-exercise cold water immersion protocols: Understanding the impact of individual body size and composition.

The use of cold water immersion (CWI) for post-exercise recovery has become increasingly prevalent in recent years with the aim to promote recovery following intense periods of training and competition. There is considerable variance reported with regards to the performance recovery benefits of CWI, and this is often attributed to differences in the CWI protocol (e.g. water temperature, immersion duration, immersion depth or mode of immersion), and type of exercise used (e.g. endurance vs sprint events). Individual differences may also impact this variance (e.g. age, gender, body size and composition, etc.); however, to date these factors have received little attention. This thesis aimed to examine how differences in CWI protocols and individual body size and composition may impact physiological and performance responses to post-exercise CWI. A series of three separate but related studies were conducted to further describe the physiological and performance responses to post-exercise CWI with the purpose of optimising the prescription of CWI for athletes. ; Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2017.
Mixed Graphical Models for Causal Analysis of Multi-modal Variables

Graphical causal models are an important tool for knowledge discovery because they can represent both the causal relations between variables and the multivariate probability distributions over the data. Once learned, causal graphs can be used for classification, feature selection and hypothesis generation, while revealing the underlying causal network structure and thus allowing for arbitrary likelihood queries over the data. However, current algorithms for learning sparse directed graphs are generally designed to handle only one type of data (continuous-only or discrete-only), which limits their applicability to a large class of multi-modal biological datasets that include mixed type variables. To address this issue, we developed new methods that modify and combine existing methods for finding undirected graphs with methods for finding directed graphs. These hybrid methods are not only faster, but also perform better than the directed graph estimation methods alone for a variety of parameter settings and data set sizes. Here, we describe a new conditional independence test for learning directed graphs over mixed data types and we compare performances of different graph learning strategies on synthetic data.
Children’s Views on Long-Term Screening for Type 1 Diabetes

There are an increasing number of medical research studies involving children, including many long-term birth cohort studies. Involving children raises many issues, and little is known about children’s own views. This study explored children’s views (N = 5,851) on participation in a long-term screening study for type 1 diabetes. The results show that children 10 to 13 years of age have in general a positive attitude to pediatric research and emphasized trust in researchers. The children stressed the importance to receive information and to be involved in decisions. The children also reported feeling concerned about blood sampling and disease risk. Researchers involved in long-term pediatric research need to address these issues to promote involvement and decrease worry.
Improving Web Browsing on Wireless PDAs Using Thin-Client Computing

Web applications are becoming increasingly popular for mobile wireless PDAs. However, web browsing on these systems can be quite slow. An alternative approach is handheld thin-client computing, in which the web browser and associated application logic run on a server, which then sends simple screen updates to the PDA for display. To assess the viability of this thin-client approach, we compare the web browsing performance of thin clients against fat clients that run the web browser locally on a PDA. Our results show that thin clients can provide better web browsing performance compared to fat clients, both in terms of speed and ability to correctly display web content. Surprisingly, thin clients are faster even when having to send more data over the network. We characterize and analyze different design choices in various thin-client systems and explain why these approaches can yield superior web browsing performance on mobile wireless PDAs.
Targeting the Ischemic Penumbra

Background— In the last 3 decades, and from a therapeutic point of view, the classical concept of ischemic penumbra based on hemodynamic and electrophysiological parameters has loosened up the rigidity of therapeutic windows in acute stroke management. Thirty years later, the ischemic penumbra is an evolved concept that presents more applications. Thus, the ischemic penumbra is a diagnostic target, allowing the extension of therapeutic windows; it is also a biochemical target, in which an intermittent bioenergetic compromise takes place, and it is a target for brain plasticity, neuroprotection, and neurorepair. Summary of Review— In this work, we review how the concept of ischemic penumbra has been evolving from its purely electrophysiological/ hemodynamic based definition to the wider metabolic-cellular-therapeutic concept that is managed today by neuroscientists.
Altered transfer RNA methylase patterns in Marek's disease tumors.

The in vitro tRNA methylase activities in liver and kidney homogenates from chicks infected with Marek's disease virus were elevated up to 3-fold compared to those in noninfected control animals. Increased enzyme activity was observed after the development of discrete tumors and was highest in isolated tumor nodules when separated from normal adjacent tissue. Organs with no visible tumor foci (lung, heart, spleen) did not possess elevated methylase activities. While extracts from both control and tumorous liver methylated heterologous methyl-deficient tRNA from Escherichia coli K-12 W-6 (tRNAMe-), only extracts from tumor-bearing livers possess methylases for the synthesis of N 7-methylguanosine, 3-methylcytidine, and 5-methyluridine. When control chick liver tRNA was the substrate, a similar pattern of results was obtained but at a lower methyl acceptance capacity. tRNA prepared from tumorous liver was approximately one-fourth as effective as control liver tRNA as a substrate for E. coli methylases.