Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Cooking on the Oxalate Content of Selected Thai Vegetables

Total and soluble oxalate content levels were measured in thirteen selected vegetables purchased from a local market in Surin Province in the northeast of Thailand. Total oxalate contents of the leaves, shoots and roots of the fresh vegetables ranged from 249.5 ± 12.1 to 7597.9 ± 77.6 mg oxalate/100g dry matter (DM) while soluble oxalate content ranged from 205.0 ± 2.3 to 2677.6 ± 19.0 mg oxalate/100g DM. Very high levels of total oxalates were found in three of the selected Thai vegetables, Polygonum odoratum (7597.9 ± 77.6 mg/100g DM), Piper aurantaucum (7026.6 ± 76.9 mg/100g DM) and Limnophila aromatica (6179.0 ± 23.6 mg/100g DM). However, the soluble oxalate content of L. aromatica was low and the highest soluble oxalate contents of fresh vegetables were found in P. odoratum, P. aurantuacum and Neptunia oleracea at 2677.6 ± 19.0, 2152.2 ± 65.3 and 1640.8 ± 3.4 mg/100g DM, respectively. Boiling the vegetables reduced the soluble oxalate content between 30.4 and 65.0%. The insoluble oxalate levels increased in eleven of the cooked vegetables while small decreases were observed in L. aromatica and N. oleracea.
Self-harm as a means to manage the public and private selves: A qualitative study of help seeking by adults

Adults (n = 25) completed online free text boxes about their self-harming behaviour. Thematic analysis identified three dominant themes: ‘managing the private self’, ‘managing the public self’ and ‘moving on’. Transcending these themes was the notion of thresholds of change. Self-harm enables people to manage both their private and public selves. When thresholds of change are surpassed, the public self communicates a need for help. Self-harm exists within a precarious balance of well-being and can be a form of self-care. Help seeking is instigated when this balance is disrupted and continued if it offers a better form of self-management than the individual’s own self-harming behaviour.
Syntactic Contexts for Finding Semantically Related Words

Finding semantically related words is a first step in the direction of automatic ontology building. Guided by the view that similar words occur in similar contexts, we looked at the syntactic context of words to measure their semantic similarity. Words that occur in a direct object relation with the verb drink, for instance, have something in common (liquidity, .). Co-occurrence data for common nouns and proper names, for several syntactic relations, was collected from an automatically parsed corpus of 78 million words of newspaper text. We used several vector-based methods to compute the distributional similarity between words. Using Dutch EuroWordNet as evaluation standard, we investigated which vector-based method and which combination of syntactic relations is the strongest predictor of semantic similarity.
Utility of ultrasonography for diagnosis of superficial swellings in buffalo (Bubalus bubalis)

We studied 72 buffalo with superficial swellings in the head (n=4), neck (n=5), chest wall (n=4), abdominal wall (n=28), limbs (n=16), gluteal region (n=8), perineal region (n=6) and udder (n=1). Ultrasonographically, the swellings varied according to type, duration, content and location. The clinical use of ultrasound to assess these superficial swellings allowed diagnosis of abscesses (n=21), hematomas (n=11), hernias (n=17), bursitis (n=13), urethral diverticula (n=6) and tumors (n=4). Ultrasonography could precisely discriminate each lesion type (sensitivity, 71–100%; specificity, 75–100%; odds ratio, 1.0–8.4; Confidence Interval, 74.2–20; and P value 0.001). The specificity for ultrasonographic evaluation of superficial swellings was 100% for hernias, urethral diverticula and tumors, whilst the lowest specificity was recorded for hematomas (75%) and abscesses (92%). In conclusion, ultrasonography provides a precise, non-invasive and fast technique for the evaluation, classification and subsequent treatment of a variety of superficial swellings in buffalo.
In Vitro Behavior of Primary Human Osteoblasts Onto Microrough Titanium Surface

Objective:The aim of this study was to evaluate in vitro the behavior and the biocompatibility of primary human osteoblasts (HOs) grown onto different implant surface. Methods and Materials:HOs were cultured onto sandblasted/acid-etched (control group) and sandblasted/acid-etched followed by coating with inorganic ions (test group) experimental titanium discs. At established times, SEM analysis, LDH assay, MTT assay, and enzyme-linked immunosorbent assay for type 1 collagen, interleukin (IL)-6, and PGE2 secretion were performed. Results:Both surfaces promote HOs adhesion and proliferation. After 21 days, cells on test surfaces are well spread, flattened, and attached by cellular extensions, whereas cells on control discs appear mainly elongated. Lower LDH levels and higher values of MTT assay are recorded for cells on test respect to control surfaces at each experimental time. Type 1 collagen release increases until 14 days, significantly decreasing at day 21 in cells grown on both surfaces. IL-6 and PGE2 secretion shows a peak in control group samples at day 7, whereas their levels do not significantly modify in both groups at days 14 and 21. Conclusion:Results indicate that the test group surface is more biocompatible, well tolerated, and suitable for supporting osteoblasts growth and proliferation.
Duration of Resuscitation Efforts and Functional Outcome After Out-of-Hospital Cardiac Arrest: When Should We Change to Novel Therapies?

Background— Functionally favorable survival remains low after out-of-hospital cardiac arrest. When initial interventions fail to achieve the return of spontaneous circulation, they are repeated with little incremental benefit. Patients without rapid return of spontaneous circulation do not typically survive with good functional outcome. Novel approaches to out-of-hospital cardiac arrest have yielded functionally favorable survival in patients for whom traditional measures had failed, but the optimal transition point from traditional measures to novel therapies is ill defined. Our objective was to estimate the dynamic probability of survival and functional recovery as a function of resuscitation effort duration to identify this transition point. Methods and Results— Retrospective cohort study of a cardiac arrest database at a single site. We included 1014 adult (≥18 years) patients experiencing nontraumatic out-of-hospital cardiac arrest between 2005 and 2011, defined as receiving cardiopulmonary resuscitation or defibrillation from a professional provider. We stratified by functional outcome at hospital discharge (modified Rankin scale). Survival to hospital discharge was 11%, but only 6% had a modified Rankin scale of 0 to 3. Within 16.1 minutes of cardiopulmonary resuscitation, 89.7% (95% confidence interval, 80.3%–95.8%) of patients with good functional outcome had achieved return of spontaneous circulation, and the probability of good functional recovery fell to 1%. Adjusting for prehospital and inpatient covariates, cardiopulmonary resuscitation duration (minutes) is independently associated with favorable functional status at hospital discharge (odds ratio, 0.84; 95% confidence interval, 0.72–0.98; P=0.02). Conclusions— The probability of survival to hospital discharge with a modified Rankin scale of 0 to 3 declines rapidly with each minute of cardiopulmonary resuscitation. Novel strategies should be tested early after cardiac arrest rather than after the complete failure of traditional measures.
Retrospective Evaluation of Hairy Cell Leukemia Patients Treated with Three Different First-Line Treatment Modalities in the Last Two Decades: A Single-Center Experience

Objective: In this study, we retrospectively analyzed the clinical outcome, treatment responses, infectious complications, and survival rates of 71 hairy cell leukemia (HCL) cases. Materials and Methods: Sixty-seven patients received a first-line treatment and 2-chlorodeoxyadenosine (cladribine-2-CdA) was administered in 31 cases, 19 patients received interferon-alpha (INF-α), splenectomy was performed in 16 cases, and rituximab was used in one. Results: Although the highest overall response rate (ORR) was observed in patients receiving 2-CdA upfront, ORRs were comparable in the 2-CdA, INF-α, and splenectomy subgroups. Relapse rates were significantly lower in patients who received first-line 2-CdA. The progression-free survival (PFS) rate with 2-CdA was significantly higher than in patients with INF-α and splenectomy, but we found similar overall survival rates with all three upfront treatment modalities. Infections including tuberculosis were a major problem. Conclusion: Although purine analogues have improved the ORRs and PFS, there is still much progress to make with regard to overall survival and relapsed/refractory disease in patients with HCL.
Methods for Molecular Surveillance of Influenza Used in Macedonia

Abstract The aim: To present and compare different Nucleic Acid Testing assays used for laboratory diagnosis of influenza virus infection in our country. Materials and methods: Respiratory samples used were nose and throat swabs. The RNA extraction was performed with a QIAamp viral RNA kit. During the season 2009–2010 the first 25 samples were tested with: conventional gel-based RT-PCR and CDC rtRT-PCR using published specific matrix and HA gene primers and probes for influenza virus typing and subtyping. Results: Of 25 samples tested with conventional RT-PCR 7(28%) were positive for influenza A, but negative for A/H1seasonal and A/H3. Retested with rtRT-PCR 9(36%) were positive for influenza A, 8(32%) were positive for A/H1pdm and 1(4%) was A/H3. Two samples positive with rtRT-PCR for influenza A were negative with RT-PCR. The sensitivity of the RT-PCR in comparison with rtRT-PCR is 100% and the specificity is 88.89%. Positive predictive value for RT-PCR is 77.78%, and negative predictive value is 100%. RT-PCR is a four-step and rtRT-PCR a one-step procedure. The turn-around time of RT-PCR is 6 hours and for rtRT-PCR it is 2 hours. Discussion and conclusion: For surveillance purposes nose and throat swabs are the more easy and practical to collect. It was proved that RT-PCR is too laborious, multi-step and time-consuming. The sensitivity of both assays is equal. The specificity of rtRT-PCR is higher. NAT assays for detection of influenza viruses have become an integral component of the surveillance programme in our country. They provide a fast, accurate and sensitive detection of influenza.
The Clinical Value of Myocardial Blood Flow Measurement*

PET provides robust and reproducible measurements of regional myocardial blood flow in milliliters per minute per gram of tissue, providing unique pathophysiologic and diagnostic information on the function of the coronary macro- and microcirculation. There is compelling evidence to suggest that in many instances abnormalities of global myocardial perfusion are demonstrated in individuals with either coronary risk factors for coronary artery disease or different myocardial diseases in the absence of angiographically demonstrable stenosis of the epicardial coronary arteries. In this context, measurement of myocardial blood flow gives unique diagnostic information regarding the function of the coronary microcirculation and provides a quantitative surrogate endpoint against which the efficacy of treatments can be established.
Interplay between structural rigidity and electrostatic interactions in the ligand binding domain of GluR2

Using molecular dynamics (MD) simulations, computational protein modifications, and a novel theoretical methodology that determines structural rigidity/flexibility (the FIRST algorithm), we investigate how molecular structure and dynamics of the glutamate receptor ligand binding domain (GluR2 S1S2) facilitate its conformational transition. S1S2 is a two‐lobe protein, which undergoes a cleft closure conformational transition upon binding an agonist in the cleft between the two lobes; hence it is expected that the mechanism of this conformational transition can be characterized as a hinge‐type. However, in the rigidity analysis one lobe of the protein is identified as a single rigid cluster while the other one is structurally flexible, inconsistent with a presumed mechanical hinge mechanism. Instead, we characterize the cleft‐closing transition as a load and lock mechanism. We find that when two cross‐cleft hydrogen bonds are disrupted the protein undergoes a rapid cleft opening transition. At the same time, the dynamical behavior of the cleft in the presence of the glutamate ligand is only weakly affected by the S652 peptide bond in its flipped conformation observed in the crystal structure. The residue E705 plays significant role in stabilization of the closed conformation via electrostatic interactions. The presence of the E705‐K730 salt bridge seems to correlate strongly withthe cleft opening transition in the MD simulations. Proteins 2008. © 2008 Wiley‐Liss, Inc.
An Engineered Metal Sensor Tunes the Kinetics of Synaptic Transmission

The Ca2+ sensor synaptotagmin-1 (syt-1) regulates neurotransmitter release by interacting with anionic phospholipids. Here we test the idea that the intrinsic kinetics of syt–membrane interactions determine, in part, the time course of synaptic transmission. To tune the kinetics of this interaction, we grafted structural elements from the slowest isoform, syt-7, onto the fastest isoform, syt-1, resulting in a chimera with intermediate kinetic properties. Moreover, the chimera coupled a physiologically irrelevant metal, Sr2+, to membrane fusion in vitro. When substituted for syt-1 in mouse hippocampal neurons, the chimera slowed the kinetics of synaptic transmission. Neurons expressing the chimera also evinced rapid and efficient Sr2+ triggered release, in contrast to the weak response of neurons expressing syt-1. These findings reveal presynaptic sensor–membrane interactions as a major factor regulating the speed of the release machinery. Finally, the chimera failed to clamp the elevated spontaneous fusion rate exhibited by syt-1 KO neurons, indicating that the metal binding loops of syt-1 regulate the two modes of release by distinct mechanisms. SIGNIFICANCE STATEMENT In calcium, synaptotagmin-1 triggers neurotransmitter release by interacting with membranes. Here, we demonstrate that intrinsic properties of this interaction control the time course of synaptic transmission. We engineered a “chimera” using synaptotagmin-1 and elements of a slower isoform, synaptotagmin-7. When expressed in neurons, the chimera slowed the rate of neurotransmitter release. Furthermore, unlike native synaptotagmin-1, the chimera was able to function robustly in the presence of strontium–a metal not present in cells. We exploited this ability to show that a key function of synaptotagmin-1 is to penetrate cell membranes. This work sheds light on fundamental mechanisms of neurotransmitter release.
Prospective study of the association between exercise-induced pulmonary haemorrhage and long-term performance in Thoroughbred racehorses.

REASONS FOR PERFORMING STUDY Exercise-induced pulmonary haemorrhage (EIPH) is associated with impaired short-term race performance but consequences to long-term race performance of Thoroughbred racehorses are unknown. Knowledge of effects of EIPH on performance over a prolonged time would inform the need for management and treatment of this disorder. OBJECTIVES To determine the relationship between EIPH detected on a single occasion and long-term athletic performance in Thoroughbred racehorses. STUDY DESIGN Prospective, longitudinal, observational epidemiological study conducted from 2003 to 2012. METHODS Seven hundred and forty-four Thoroughbred racehorses underwent a single tracheobronchoscopic examination to determine presence and severity of EIPH in 2003. Following retirement of all the horses from racing, career after examination and lifetime performance data (including career duration, earnings, starts, wins and placings) were abstracted from a commercial database. The association between presence and severity of EIPH and individual performance variables were analysed using survival analysis, linear regression and negative binomial regression. RESULTS No association was detected between the presence of any EIPH (grade ≥1) and all measures of long-term performance examined except that horses with EIPH (grade ≥2) had fewer earnings after endoscopic examination than did horses with mild EIPH or no EIPH (grades ≤1). Multiple associations were detected between the most severe form of EIPH (grade 4) and measures of long-term performance suggesting that the severity of EIPH commonly associated with epistaxis adversely affects either the horse's opportunity to race or physiologic capacity to race. CONCLUSIONS We conclude that there is no association between EIPH grades 0, 1, 2 and 3 and long-term racing performance of Thoroughbred racehorses. These results are based on a single endoscopic evaluation of EIPH grade made during a horse's career. Further studies are required to determine the reasons for an association of severe (grade 4) EIPH with impaired long-term race performance.
Expression of xenobiotic and steroid hormone metabolizing enzymes in human breast carcinomas

The potential to metabolize endogenous and exogenous substances may influence breast cancer development and tumor growth. Therefore, the authors investigated the protein expression of Glutathione S‐transferase (GST) isoforms and cytochrome P450 (CYP) known to be involved in the metabolism of steroid hormones and endogenous as well as exogenous carcinogens in breast cancer tissue to obtain new information on their possible role in tumor progression. Expression of GST pi, mu, alpha and CYP1A1/2, 1A2, 3A4/5, 1B1, 2E1 was assessed by immunohistochemistry for primary breast carcinomas of 393 patients from the German GENICA breast cancer collection. The percentages of positive tumors were 50.1 and 44.5% for GST mu and CYP2E1, and ranged from 13 to 24.7% for CYP1A2, GST pi, CYP1A1/2, CYP3A4/5, CYP1B1. GST alpha was expressed in 1.8% of tumors. The authors observed the following associations between strong protein expression and histopathological characteristics: GST expression was associated with a better tumor differentiation (GST mu, p = 0.018) and with reduced lymph node metastasis (GST pi, p = 0.02). In addition, GST mu expression was associated with a positive estrogen receptor and progesterone receptor status (p < 0.001). CYP3A4/5 expression was associated with a positive nodal status (p = 0.018). Expression of CYP1B1 was associated with poor tumor differentiation (p = 0.049). Our results demonstrate that the majority of breast carcinomas expressed xenobiotic and drug metabolizing enzymes. They particularly suggest that GST mu and pi expression may indicate a better prognosis and that strong CYP3A4/5 and CYP1B1 expression may be key features of nonfavourable prognosis. © 2006 Wiley‐Liss, Inc.
Efferent connections of the dorsal cortex of the lizard Gekko gecko studied with Phaseolus vulgaris‐leucoagglutinin

The efferent connections from the dorsal cortex of the lizard Gekko gecko have been studied with the anterograde tracer Phaseolus vulgaris‐leucoagglutinin. It appeared that the dorsal cortex is not a homogeneous structure as far as the efferent connections are concerned. All parts of the dorsal cortex project to the septum. All parts except the most medial project to the dorsal ventricular ridge, amygdala, nucleus periventricularis hypothalami, area lateralis hypothalami, and the anterior olfactory nucleus. The most medial part, in addition to the septal projections, is connected with the medial cortex and the contralateral medial and dorsal cortices. From the rostral part additional projections could be traced to the nucleus dorsolateralis hypothalami, nucleus ventromedialis thalami, nucleus dorsolateralis thalami, striatum, pallial thickening, medial cortex, nucleus olfactorius anterior, and the main and accessory olfactory bulbs.
The Potential of Citizen Observatories for Improving Spatial Measurements of Rainfall in Cities

Urban pluvial flooding occurs when the run-off converted rainfall exceeds the capacity of the sewer or stormwater system (Houston et al., 2011). This can result in damage to ecology, infrastructure, disruption to human activities, injuries and in the worst-case scenario, loss of life (Biniyam et al., 2017). With the expected increase in the world’s population living in urban areas to 68% by 2050 (UN, 2018) and a more frequent occurrence of extreme weather events with a longer duration and higher intensity in the future (IPCC, 2012), there is a need to improve early warning system and disaster management (Restrepo-Estrada et al., 2017). Lopez et al. (2005) mentions that one of the key factors in hydrological models to determine accurate flood estimates is to have accurate rainfall input. However, many urban areas might lack this information because sensors are not available, or the number of sensors is too few to cover the entire region with an acceptable resolution (Restrepo-Estrada et al., 2017). Kidd et al. (2017) mentions that the density of rain gauges varies per region, with Europe and Eastern-Asia (including Japan) having a decent coverage by rain gauges, while the rest of the world has a sparse coverage of rain gauges. This study assesses the potential of citizen observatories for improving the spatial measurements of rainfall in comparison to a single professional station. Two types of citizen observatories are used, semi-professional stations (TU Delft) and citizen weather stations (Netatmo), that are located near the city of Rotterdam. In total there are 9 TU Delft stations and 73 Netatmo stations in a region of 256.7 km2. Based on a spatial variance analysis between these two types of citizen observatories and a professional station (KNMI) in the region, weighing factors are determined in order to merge and interpolate the data from the citizen observatories into a single rainfall map. This interpolated map is then compared to the radar rainfall maps, which are bias-corrected based on a network of professional ground stations (Overeem et al., 2016), and provide rainfall data with a 1x1 km spatial resolution. The baseline for improvement comes from the assumption that the rainfall measured by the KNMI station is uniform over the entire study area. By comparing the differences between KNMI and radar and citizen observatories and radar, it can be assessed whether the citizen observatories are an improvement. The results show that the interpolated rainfall maps are better at capturing the spatial structure of the rainfall event, both on the small-scale (10-minute timestep) and event-scale (total accumulation). When it comes to the actual rainfall values, it became clear that rainfall intensities within a 4 km radius from the KNMI station were better represented by the KNMI station while after a distance of 8 km, the citizen stations clearly helped give a better representation.