Miracle-dz/UniFAR-FTUs huggingface dataset:
Thin-layer chromatography in medicinal chemistry

Abstract Among widely used chromatographic methods modern thin-layer chromatography is not only the simplest to perform but is also considered as respectable analytical method in various phases of drug discovery and development processes such as monitoring of synthesis, identification of bioactive substances from various natural sources and their isolation and purification, determination of lipophilicity and other physico-chemical parameters, quantitative structure-activity relationship studies, bioautography, as well as qualitative and quantitative analysis of drugs and their metabolites. An overview of recently published papers dealing with application of thin-layer chromatography in medicinal chemistry is presented. GRAPHICAL ABSTRACT
Dosimetric evaluation of MRI-based treatment planning for prostate cancer

The purpose of this study is to evaluate the dosimetric accuracy of MRI-based treatment planning for prostate cancer using a commercial radiotherapy treatment planning system. Three-dimensional conformal plans for 15 prostate patients were generated using the AcQPlan system. For each patient, dose distributions were calculated using patient CT data with and without heterogeneity correction, and using patient MRI data without heterogeneity correction. MR images were post-processed using the gradient distortion correction (GDC) software. The distortion corrected MR images were fused to the corresponding CT for each patient for target and structure delineation. The femoral heads were delineated based on CT. Other anatomic structures relevant to the treatment (i.e., prostate, seminal vesicles, lymph notes, rectum and bladder) were delineated based on MRI. The external contours were drawn separately on CT and MRI. The same internal contours were used in the dose calculation using CT- and MRI-based geometries by directly transferring them between MRI and CT as needed. Treatment plans were evaluated based on maximum dose, isodose distributions and dose–volume histograms. The results confirm previous investigations that there is no clinically significant dose difference between CT-based prostate plans with and without heterogeneity correction. The difference in the target dose between CT- and MRI-based plans using homogeneous geometry was within 2.5%. Our results suggest that MRI-based treatment planning is suitable for radiotherapy of prostate cancer.
Intraspecific root and leaf trait variation with tropical forest successional status: consequences for community-weighted patterns

Quantifying the dimensions and magnitude of intraspecific root trait variation is key to understanding the functional trade-offs in the belowground plant strategies of tropical forest trees. Additionally, accurately measuring how belowground functional trait variation relates to soil environment and forest age is crucial to tropical forest modeling efforts. We sampled leaf and root morphologies from 423 juvenile trees of 72 species from 14 Angiosperm families along a 6.6 km transect that corresponded to an environmental gradient in decreasing soil fertility and texture with increasing forest age. We observed within-lineage conservative functional trait-shifts in root and leaf morphological traits along the transect. From secondary to primary forest, average leaf area increased 7 cm2 and average root system diameter increased 0.4 mm. Mean specific leaf area decreased by 0.8 m2 kg−1, specific root length decreased by 3.5 m kg−1, and root branching intensity decreased by 0.3 tips cm−1. Leaf thickness and root tissue density showed no change. We coupled trait measurements to a network of 164 1/16th-ha plots across a Chinese tropical forest reserve, to scale individual trait measurements up to the community-level, accounting for forest age. For most traits, intraspecific trait variation negatively covaried with species compositional turnover between plots in younger versus older forest to compound and create greater community-weighted differences in trait values than would be observed if intraspecific variation in traits with forest age was not accounted for. Summary Root morphologies are variable with local scale variation in soil fertility and texture. Accurately understanding broader (i.e. forest)-scale patterns in root functional traits, requires attention to underlying environmental variation in soil resources, which interacts with environmental filtering of plant communities.
Neural Domain Adaptation for Biomedical Question Answering

Factoid question answering (QA) has recently benefited from the development of deep learning (DL) systems. Neural network models outperform traditional approaches in domains where large datasets exist, such as SQuAD (ca. 100,000 questions) for Wikipedia articles. However, these systems have not yet been applied to QA in more specific domains, such as biomedicine, because datasets are generally too small to train a DL system from scratch. For example, the BioASQ dataset for biomedical QA comprises less then 900 factoid (single answer) and list (multiple answers) QA instances. In this work, we adapt a neural QA system trained on a large open-domain dataset (SQuAD, source) to a biomedical dataset (BioASQ, target) by employing various transfer learning techniques. Our network architecture is based on a state-of-the-art QA system, extended with biomedical word embeddings and a novel mechanism to answer list questions. In contrast to existing biomedical QA systems, our system does not rely on domain-specific ontologies, parsers or entity taggers, which are expensive to create. Despite this fact, our systems achieve state-of-the-art results on factoid questions and competitive results on list questions.
A common neural code for similar conscious experiences in different individuals

Significance Although in our daily lives we engage in many of the same activities as others, we are not privy to their conscious experiences, and can only understand them through their self-reports. Patients who are conscious, but are unable to speak or exhibit willful behavior, are, therefore, unable to report their conscious experiences to others. Indeed, in most cases, it is impossible to know whether they are conscious or not. We introduce a neural index that, in a group of healthy participants, predicted each individual’s conscious experience. Moreover, this approach provided strong evidence for intact conscious experiences in a brain-injured patient who had remained behaviorally nonresponsive for 16 y. These findings have implications for understanding the common basis of human consciousness. The interpretation of human consciousness from brain activity, without recourse to speech or action, is one of the most provoking and challenging frontiers of modern neuroscience. We asked whether there is a common neural code that underpins similar conscious experiences, which could be used to decode these experiences in the absence of behavior. To this end, we used richly evocative stimulation (an engaging movie) portraying real-world events to elicit a similar conscious experience in different people. Common neural correlates of conscious experience were quantified and related to measurable, quantitative and qualitative, executive components of the movie through two additional behavioral investigations. The movie’s executive demands drove synchronized brain activity across healthy participants’ frontal and parietal cortices in regions known to support executive function. Moreover, the timing of activity in these regions was predicted by participants’ highly similar qualitative experience of the movie’s moment-to-moment executive demands, suggesting that synchronization of activity across participants underpinned their similar experience. Thus we demonstrate, for the first time to our knowledge, that a neural index based on executive function reliably predicted every healthy individual’s similar conscious experience in response to real-world events unfolding over time. This approach provided strong evidence for the conscious experience of a brain-injured patient, who had remained entirely behaviorally nonresponsive for 16 y. The patient’s executive engagement and moment-to-moment perception of the movie content were highly similar to that of every healthy participant. These findings shed light on the common basis of human consciousness and enable the interpretation of conscious experience in the absence of behavior.
Progress of Research on Potential Vorticity and its Inversion

In this paper potential vorticity (PV) and potential vorticity inversion (PVI) and their application in the cyclogenesis and mesoscale meteorological phenomena are reviewed. PV has been served as a powerful and useful dynamic tracer for the understanding of the large-scale dynamics and synoptic variations in the atmosphere and oceans. Significant progress has been made on the application of PV in recent decades there has been a substantial amount of work done on PV in a general moist atmosphere. The GMPV is defined for a real atmosphere by introducing a generalized potential temperature instead of the potential temperature or equivalent potential temperature. Such a generalization can depict the moist effect on PV anomaly in the nonuniformly saturated atmosphere. Apart from PV, its inversion theory is also widely accepted as a useful tool in atmospheric diagnostics and numerical forecasting. If the suitable balanced models are chosen, the equations of potential vorticity inversion can be sufficient to deduce, diagnostically, all the other dynamical fields, such as winds, temperatures, geopotential heights, static stabilities, and vertical velocities, under a suitable balance condition. Several common kinds of potential vorticity inversion operators, and the associated balanced models, are introduced in this paper. It is confirmed that the potential vorticity and its inversion theory not only play an important role in studying the evolution and development of weather system, but also would give new content in the present weather forecasting system.
Advanced polyhedral discretization methods for poromechanical modelling

In this manuscript we focus on novel discretization schemes for solving the coupled equations of poroelasticity and we present analytical and numerical results for poromechanics problems relevant to geoscience applications. We propose to solve these problems using Hybrid High-Order (HHO) methods, a new class of nonconforming high-order methods supporting general polyhedral meshes. This Ph.D. thesis was conjointly founded by the Bureau de recherches geologiques et minieres (BRGM) and LabEx NUMEV. The coupling between subsurface flow and geomechanical deformation is a crucial research topic for both cofunding institutions.
Diagnostic specificity and sensitivity of PIVKAII, GP3, CSTB, SCCA1 and HGF for the diagnosis of hepatocellular carcinoma in patients with alcoholic liver cirrhosis

Introduction Despite some new treatment possibilities, the improvement in survival rate for hepatocellular carcinoma (HCC) patients is still poor due to late diagnosis. The aim of this study was to investigate the diagnostic sensitivity and specificity of protein induced by vitamin K absence or antagonist-II (PIVKAII), Glypican-3 (GP3), Cystatin B (CSTB), squamous cell carcinoma antigen 1 (SCCA1) and hepatocyte growth factor (HGF) as potential tumour markers for HCC in patients with alcoholic liver cirrhosis (ALC) using imaging techniques (MSCT and MRI) as reference standards. Patients and methods Eighty-three participants were included: 20 healthy volunteers, 31 patients with ALC and 32 patients with HCC. Peripheral blood sampling was performed for each participant, and serum concentrations of PIVKAII, GP3, CSTB, SCCA1 and HGF were determined using commercial ELISA kits. Results Only serum concentrations of PIVKAII were significantly higher in HCC patients as compared with ALC and healthy controls (cut-off: 2.06 µg/L; AUC: 0.903), whereas individual diagnostic performance of other individual compounds was inadequate. The ‘best’ combination of tumour markers in our study includes all tested markers with AUC of 0.967. Conclusion While novel diagnostic tumour markers are urgently needed, the examined potential tumour markers, with the exception of PIVKAII seem to be inadequate for diagnosing HCC in ALC. Furthermore, probably the future is in finding the best optimal combination of tumour markers for diagnosing HCC based on cost-effectiveness.
Antimicrobial Evaluation of the Polyisoprenylated Benzophenones Nemorosone and Guttiferone A

Polyisoprenylated benzophenones have been isolated from plants, particularly in the Clusiaceae family, and their biological properties recently have received considerable attention from a pharmacological point of view. The aim of the study was to investigate the polyisoprenylated benzophenones, nemorosone and guttiferone A, for their antimicrobial effect against a panel of bacteria, fungi and protozoan parasites. They showed a moderate activity against the Gram‐positive bacterium Staphylococcus aureus, while no activity was demonstrated against Escherichia coli and the fungi Trichophyton rubrum and Candida albicans. An interesting activity was found for Plasmodium falciparum with IC50 values lower than 1 μm, while cytotoxicity on MRC‐5 cells revealed CC50 values of 15.5 and 12.0 μm, respectively, for nemorosone and guttiferone A. Copyright © 2011 John Wiley & Sons, Ltd.
GINA guidelines on asthma and beyond *

Clinical guidelines are systematically developed statements designed to help practitioners and patients make decisions regarding the appropriate health care for specific circumstances. Guidelines are based on the scientific evidence on therapeutic interventions. The first asthma guidelines were published in the mid 1980s when asthma became a recognized public health problem in many countries. The Global Initiative on Asthma (GINA) was launched in 1995 as a collaborative effort between the NHLBI and the World Health Organization (WHO). The first edition was opinion‐based but updates were evidence‐based. A new update of the GINA guidelines was recently available and it is based on the control of the disease. Asthma guidelines are prepared to stimulate the implementation of practical guidelines in order to reduce the global burden of asthma. Although asthma guidelines may not be perfect, they appear to be the best vehicle available to assist primary care physicians and patients to receive the best possible care of asthma.
A Hausdorff dimension for finite sets

The classical Hausdorff dimension of finite or countable sets is zero. We define an analog for finite sets, called finite Hausdorff dimension which is non-trivial. It turns out that a finite bound for the finite Hausdorff dimension guarantees that every point of the set has "nearby" neighbors. This property is important for many computer algorithms of great practical value, that obtain solutions by finding nearest neighbors. We also define an analog for finite sets of the classical box-counting dimension, and compute examples. The main result of the paper is a Convergence Theorem. It gives conditions under which, if a sequence of finite sets converges to a compact set (convergence of compact subsets of Euclidean space under the Hausdorff metric), then the finite Hausdorff dimension of the finite sets will converge to the classical Hausdorff dimension of the compact set.
Effects of Intravenous Sodium Amobarbital Vs Lidocaine on Pain and Sensory Abnormalities in Patients With Spinal Cord Injury

Abstract Objective: To compare the responses of patients with spinal cord injury (SCI) in regards to pain and sensory abnormalities to single blinded intravenous (IV) infusions of normal saline, sodium amobarbital, and lidocaine. Setting: Inpatient pain unit. Study Design: Retrospective chart review. Methods: Demographic data, body maps marking pain areas, pain ratings, standardized history and detailed examination were collected on admission in 5 patients with SCI and pain. IV normal saline was followed by either IV sodium amobarbital or lidocaine, respectively, (patients, but not the administering physician, were blinded to the order of the drugs). Spontaneous pain ratings and sensory abnormalities to light touch, pinprick and cold were documented at baseline and immediately after each infusion. Results: Sodium amobarbital decreased spontaneous pain by 73% (vs 46% with lidocaine) and normalized sensory abnormalities at or above the level of injury in 3 patients (as compared to just 1 patient with lidocaine), 2 of whom had transitional zone allodynia/hyperalgesia. Conclusion: In this small study, the analgesic effect of sodium amobarbital and its ability to modify sensory abnormalities appeared superior to that of lidocaine.
BDNF variability in opioid addicts and response to methadone treatment: preliminary findings

Brain‐derived neurotrophic factor (BDNF) signaling pathways have been shown to be essential for opioid‐induced plasticity. We conducted an exploratory study to evaluate BDNF variability in opioid addict responders and nonresponders to methadone maintenance treatment (MMT). We analyzed 21 single nucleotide polymorphisms (SNPs) across the BDNF genomic region. Responders and nonresponders were classified by means of illicit opioid consumption detected in random urinalysis. Patients were assessed by a structured interview (Psychiatric Research Interview for Substance and Mental Disorders (PRISM)‐DSM‐IV) and personality was evaluated by the Cloninger’s Temperament and Character Inventory. No clinical, environmental and treatment characteristics were different between the groups, except for the Cooperativeness dimension (P < 0.001). Haplotype block analysis showed a low‐frequency (2.7%) haplotype (13 SNPs) in block 1, which was more frequent in the nonresponder group than in the responder group (4/42 vs. 1/135; Pcorrected = 0.023). Fine mapping in block 1 allows us to identify a haplotype subset formed by only six SNPs (rs7127507, rs1967554, rs11030118, rs988748, rs2030324 and rs11030119) associated with differential response to MMT (global P sim = 0.011). Carriers of the CCGCCG haplotype had an increased risk of poorer response, even after adjusting for Cooperativeness score (OR = 20.25 95% CI 1.46–280.50, P = 0.025). These preliminary results might suggest the involvement of BDNF as a factor to be taken into account in the response to MMT independently of personality traits, environmental cues, methadone dosage and psychiatric comorbidity.
Altered Autonomic Support of Arterial Blood Pressure With Age in Healthy Men

Background—Primary aging is associated with changes in the autonomic nervous system (ANS), but the functional significance of these changes for systemic circulatory control of arterial blood pressure (BP) is unknown. We tested the hypothesis that ANS support of BP is altered in healthy older humans. Methods and Results—A total of 23 young (aged 24±1 years; systolic/diastolic BP, 126±2/66±1 mm Hg) and 16 older (aged 65±1 years; systolic/diastolic BP, 125±3/62±2 mm Hg) healthy men were studied before and during ganglionic blockade (intravenous trimethaphan). The reduction in mean BP (radial artery catheter) with trimethaphan was almost twice as great in the older men (−33±2 versus −19±2 mm Hg; −40% versus −22% of baseline;P <0.01) due to a lack of increase in heart rate (3±2 versus 25±2 bpm;P <0.001) and cardiac output (−0.42±0.19 versus 1.01±0.26 L/min;P <0.001); the decreases in systemic vascular resistance were not different. The absence of tachycardia in the older men was associated with reduced baseline heart rate variability (HRV, P <0.05); the change in heart rate with trimethaphan correlated with the standard deviation of the R-R intervals (HRVSD R-R interval;r =0.57, P <0.001). Among individual subjects (pooled groups), the reductions in mean BP with trimethaphan were most strongly related to measures of sympathetic activity (r =0.58 to 0.67, P <0.005), change in mean BP with intravenous phenylephrine (r =0.57, P <0.001), and HRVSD R-R interval (r =−0.40, P <0.01). Conclusions—ANS support of BP is altered with age in healthy men due to less cardiac vagal inhibition of heart rate and cardiac output. Basal sympathetic activity and &agr;-adrenergic vascular sensitivity are also key physiological correlates of ANS support of BP in healthy men.
Cross-generational fitness benefits of mating and male seminal fluid

In many species, the physical act of mating and exposure to accessory gland proteins (Acps) in male seminal fluid reduces female survival and offspring production. It is not clear what males gain from harming their sexual partners or why females mate frequently despite being harmed. Using sterile strains of Drosophila melanogaster that differ in their production of Acps, we found that both the physical act of mating and exposure to male seminal fluid in mothers increase the fitness of daughters. We show that the changes in daughter fitness are mediated by parental effects, not by sexual selection involving good genes or owing to variation in maternal egg production. These results support the idea that male harm of females might partly evolve through cross-generational fitness benefits.
Frequency of Stillbirths in a Tertiary Care Hospital, Karachi

Background and Objective: Pakistan accounts for the highest stillbirth rate in the world. Therefore, this observational study was planned to determine the prevalence of stillbirths and its associated demographic characteristics in the given context. Hence our objective included: To determine the frequency of stillbirths with reference to parity and gestational age in a tertiary care public hospital, Karachi. To determine the socio-demographic characteristics of families with stillbirths. Methods: All pregnant mothers who delivered stillbirth babies at Gynaecology and Obstetrics ward of Jinnah Postgraduate Medical Center, Karachi a tertiary care facility were prospectively enrolled from October 2012 to September 2013. Deliveries occurred before 28 weeks of gestational age were excluded. Gestational age was confirmed from hospital record and attending physicians. Data was collected on predesigned proforma and analyzed using descriptive statistics. Results: Among 7708 registered deliveries, 137 were stillbirths. A total of 84 mothers were primiparous and 12% of mothers were below 20 years at the time of delivery. Majority of stillbirths were macerated type (80.3%) and 20% were fresh stillbirth. About 55% of still births occurred between 33-37 weeks and 20% between 28-32 weeks. Almost 80% (109) of stillbirths were low birth weight and only 20% (28) were normal birth weight. Conclusion: This study shows that stillbirths are more common in primiparous mothers in a given context. Conducting awareness sessions with special focus on antenatal and obstetrical care of primiparous may be helpful to reduce still births.