Miracle-dz/UniFAR-FTUs huggingface dataset:
Compartmental model of 18F-choline

The MADEIRA Project (Minimizing Activity and Dose with Enhanced Image quality by Radiopharmaceutical Administrations), aims to improve the efficacy and safety of 3D functional imaging by optimizing, among others, the knowledge of the temporal variation of the radiopharmaceuticals' uptake in and clearance from tumor and healthy tissues. With the help of compartmental modeling it is intended to optimize the time schedule for data collection and improve the evaluation of the organ doses to the patients. Administration of 18F-choline to screen for recurrence or the occurrence of metastases in prostate cancer patients is one of the diagnostic applications under consideration in the frame of the project. PET and CT images have been acquired up to four hours after injection of 18F-choline. Additionally blood and urine samples have been collected and measured in a gamma counter. The radioactivity concentration in different organs and data of plasma clearance and elimination into urine were used to set-up a compartmental model of the biokinetics of the radiopharmaceutical. It features a central compartment (blood) exchanging with organs. The structure describes explicitly liver, kidneys, spleen, plasma and bladder as separate units with a forcing function approach. The model is presented together with an evaluation of the individual and population kinetic parameters, and a revised time schedule for data collection is proposed. This optimized time schedule will be validated in a further set of patient studies.
Constant signal tracking for state constrained dynamic systems

We deal with the possibility of tracking constant reference signals for a linear time-invariant dynamic system in the presence of state constraints. We resort to the theory of invariant sets due to their capability of well handling this kind of problems. We focus on the determination of suitable sets for the attainable steady state values and of suitable control laws which guarantee that every possible output steady state value belonging to this set can be reached from any initial state belonging to a proper set. Then, based on recent results on the possibility of associating to these explicit smooth control laws, we derive an explicit controller which allows the system to asymptotically track constant reference signals and guarantees that no constraint violation occurs. Finally, we report an example of the implementation of the proposed control law.
Epidemiology of Hepatitis C in North Cyprus

Ad dress for Cor res pon den ce: Meryem Güvenir MD, Near East University, Vocational School of Health Services, Department of Microbiology, Lefkoşa, North Cyprus E-mail: meryemguvenir@hotmail.com ORCID ID: orcid.org/0000-0002-9702-9947 Re cei ved: 27.10. 2017 Ac cep ted: 29.12. 2017 ©Copyright 2018 by Viral Hepatitis Society / Viral Hepatitis Journal published by Galenos Publishing House. Introduction
Enabling Technologies for Synthetic Biology: Gene Synthesis and Error-Correction from a Microarray-Microfluidic Integrated Device

Enabling Technologies for Synthetic Biology: Gene Synthesis and Error-Correction from a MicroarrayMicrofluidic Integrated Device by Ishtiaq-es-Saaem Department of Biomedical Engineering Duke University Date:_______________________ Approved: ___________________________ Jingdong Tian, Co-Supervisor ___________________________ Thomas LaBean, Co-Supervisor ___________________________ William Reichert ___________________________ Stefan Zauscher ___________________________ Munir Alam An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biomedical Engineering in the Graduate School of Duke University 2011 Copyright by Ishtiaq-es-Saaem 2011
Assessment of Nutritional Status and its Determinants among Students of Army Public School, Okara, Pakistan

Background: Malnutrition is a health problem affecting growth and development of young children. Children under 15 years of age are the main victims of malnutrition. Malnutrition is attributed to a series of diverse etiological factors. Objective: To determine the nutritional status of the children of various age groups of school going children of Army Public School and to find out the association of socio-demographic variables and dietary habits with nutritional status. Methodology: It was a descriptive cross-sectional study conducted at Army Public School, Okara. Sample was selected through non-probability consecutive sampling. Duration of study was 6 months (Dec 2017 to May 2018). The study was conducted after getting formal approval from Institutional Ethical Review Board AFPGMI. The children were randomly selected for study from the enrollment register available in the principal’s office. Participation in the study was voluntary with guaranteed confidentiality. The participants were given full right to quit study without mentioning reason at any time during data collection. After ruling out the exclusion criteria, 500 children fulfilling inclusion criteria were selected for study. An informed written consent was obtained from all selected children and their parents to take part in the study. Data for the assessment of nutritional status was obtained using anthropometry, biochemical laboratory test and eating habits / food preferences of the children. Results: In our study, mean age of children included in the study was 9.58±1.72 years. Out of 500 children, 252 (50.2%) were male while 248 (49.8%) female. The mean height of children was 134.88±11.69 cm. The mean weight of children was 30.25±8.47 kg. The mean OFC of children was 51.43±1.75 cm. Out of total 500 children, 85 (17%) were having BMI less than 18.5, 338 (67.6%) were having BMI within 18.5– 24.9 while 77 (15.4%) children having BMI within 2529.9. None of child was observed with BMI of ≥30. Among 85 children with below normal BMI, 63 had mild malnutrition (BMI between 17-18.4), 19 had moderate malnutrition (BMI 16-16.9) while 3 had severe malnutrition (BMI < 16) Conclusion: Malnutrition is a significant public health problem among preschool and school going children. And improving socio-economic condition along with literacy of mothers and preventing infections through personal hygiene might help in improving the nutritional status of children.
Safety and Efficacy Outcomes of Bioresorbable Scaffolds in Long Segment Coronary Lesions

Introduction: There is limited knowledge about the use of bioresorbable scaffolds (BRSs) in long segment coronary artery lesions. We aimed to evaluate the clinical outcomes of BRS-BRS and drug eluting stents (DESs)-BRS overlapping applications. Patients and Methods: Cross-sectional, single-center study between 2013 and 2016 enrolled 97 patients and 100 lesions scheduled for BRS placement in long segment lesions (> 28 mm). BRS-BRS overlap was performed in 30 patients and 30 lesions, DES-BRS overlap was performed in 67 patients and 70 lesions. Acute procedural success and major adverse cardiac events (MACE) (death, stent thrombosis, and target lesion reintervention) were assessed. Results: Acute procedural success was 97.1% in the overall group. MACE was observed in 6 patients (6.2%) in the entire group, 4 (5.9%) in the DES-BRS group, and 2 (6.6%) in the BRS-BRS group. Conclusion: BRS use might be a safe and effective option for the treatment of long segment lesions. Both BRS-BRS overlap and BRS-DES overlap may be performed with short overlap segment.
Propagation and interaction of waves in a relaxing gas

Propagation of disturbances through a uniform region of a relaxing gas in a duct with spatially varying cross section is analysed using the methods of relatively undistorted waves and weakly nonlinear geometrical optics. Particular attention is focused on situations when the disturbance amplitude is finite, arbitrarily small and not so small. In certain situations a complete history of the evolutionary behaviour of waves including weak shocks can be traced out. The asymptotic decay laws for weak shocks in a non-relaxing gas are exactly recovered. The damping effects of relaxation and non-planar wavefront configurations on the distortion, attenuation and shock formation of pulses, as they propagate, are described in detail. In the small-amplitude high-frequency limit, a solution up to the second order is obtained and numerical computations are carried out for typical values of the physical parameters involved in the solution. Transport equations are derived for signals having all possible wave modes which are mutually coupled and interact resonantly among themselves. The progressive wave approach describes the far field behaviour which is governed by the generalized Burger’s equation.
The Dutch Acute Stroke Audit: Benchmarking acute stroke care in the Netherlands

Abstract Introduction In the nationwide Dutch Acute Stroke Audit (DASA), consecutive patients with acute ischaemic stroke (AIS) and intracranial haemorrhage (ICH) are prospectively registered. Acute stroke care is a rapidly evolving field in which intravenous thrombolysis (IVT) and intra-arterial thrombectomy (IAT) play a crucial role in increasing odds of favourable outcome. The DASA can be used to assess the variation in care between hospitals and develop ‘best practice’ in acute stroke care. Patients and methods: We describe the initiation and design of the DASA as well as the results from 2015 and 2016. Results In 2015 and 2016, 55,854 patients with AIS and 7727 patients with ICH were registered in the DASA. Treatment with IVT was administered to 10,637 patients (with an increase of 1.3% in 2016) and 1740 patients underwent IAT (with an increase of 1% in 2016). Median door-to-needle time for IVT and median door-to-groin time for IAT have decreased from 27 to 25 min and 66 to 64 min, respectively. Mortality during admission was 4.9% in patients with AIS, whereas 26% of patients with ICH died. Modified Rankin Scale score at three months was registered in 49% of AIS patients and 45% of ICH patients. Discussion During the nationwide DASA, time to treatment is reduced for IVT as well as IAT. With the rapidly evolving treatment of acute stroke care, the DASA can be used to monitor the quality provided on patient- and hospital level. Conclusion Increasing completeness of registration of the outcome, in combination with adjustment for patient-related factors, is necessary to define and further improve the quality of the acute stroke care.
Heroin Use Is Associated with Suppressed Pro-Inflammatory Cytokine Response after LPS Exposure in HIV-Infected Individuals

Background Opioid use is associated with increased incidence of infectious diseases. Although experimental studies have shown that opioids affect various functions of immune cells, only limited data are available from human studies. Drug use is an important risk factor for HIV transmission; however no data are available whether heroin and/or methadone modulate immune response. Therefore, we examined the effect of heroin and methadone use among HIV-infected individuals on the production of cytokines after ex vivo stimulation with various pathogens. Methods Treatment naïve HIV-infected individuals from Indonesia were recruited. Several cohorts of individuals were recruited: 1) using heroin 2) receiving methadone opioid substitution 3) using heroin over 1 year ago and 4) controls (never used opioids). Whole blood was stimulated with Mycobacterium tuberculosis, Candida albicans and LPS for 24 to 48 hours. Cytokine production (IL-1 β, IL-6, IL-10, IFN-α, IFN-γ and TNF-α) was determined using multiplex beads assay. Results Among 82 individuals, the cytokine levels in unstimulated samples did not differ between groups. Overall, heroin users had significantly lower cytokine response after exposure to LPS (p<0.05). After stimulation with either M. tuberculosis or C. albicans the cytokine production of all groups were comparable. Conclusion The cytokine production after exposure to LPS is significantly down-regulated in HIV-infected heroin users. Interesting, methadone use did not suppress cytokine response, which could have implications guidelines of opioid substitution.
MAGMA: Generalized Gene-Set Analysis of GWAS Data

By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn’s Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn’s Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn’s Disease data was found to be considerably faster as well.
Transcriptome and Genome Size Analysis of the Venus Flytrap

The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin’s studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.
Services provided to relatives of patients admitted to a psychiatric hospital : an assessment of family satisfaction

This study explores family satisfaction with services provided to them on their relatives' adnllssion to Valkenberg Psychiatric Hospital in Cape Town. The rationale for doing this research arose from the researcher's encounters with families of psychiatric patients and the perceived lack of involvement of the professionals with the families. In addition, a needs assessment was done to establish the need for family groups. The literature review traced the psychiatric services from the earlier custodial orientation, the subsequent deinstitutionalisation of the services resulting in the families becoming the primary caregivers of their mentally ill relatives, to the emphasis of the biopsychosocial model in the recently established community services. Review of the treatment models indicated supportive family education as the primary form of intervention to ensure compliance, aid the recuperation process, enhance the quality of life for the patient and their families and to equip the families to cope with the illness. A survey method was employed to gather quantitative and qualitative data via questionnaires and face-to-face interviews with 31 relatives of 24 patients who had been admitted during January, February, and in March 1995 to the male and female admission ·units (wards 9, 10, 14, 15 and 16) at Valkenberg psychiatric hospital in Cape Town. A non-probability convenience sampling procedure, based on the availability and accessibility of the relatives to attend an office interview, was used. Findings from prior studies as well as from this current study have shown a lack of professional involvement with the families in relation to the treatment programme of their mentally ill relatives. The majority of the respondents were not informed about the implications of the illness and the effect of treatment and most of the respondents lacked
Prospective study to evaluate the risk factors associated with male infertility at tertiary care centre

Background: Infertility is a condition with psychological, economic, medical implications resulting in mental trauma, stress particularly in social set up like ours, with strong emphasis on child bearing. According to the International Committee for Monitoring Assisted Reproductive Technology, World Health Organization (WHO), Infertility is disease of reproductive system defined by failure to achieve the clinical pregnancy after 12 months or more of regular unprotected sexual intercourse.Methods: This study was conducted in Department of Surgery in Jawaharlal Nehru Medical College, Aligarh from January 2017 to December 2017 on 120 patients to study the clinical profile, causes of male infertility and to evaluate the risk factors associated with it.Results: There were 54 (45%) patients with azoospermia and 66 (55%) had oligospermia. Out of them 52 (43.3%) had sperm counts of 1-8 millions/ml and 14 (11.6%) had sperm count between >9-15 millions/ml. 46 (38.3%) patients had low testosterone level. 86 of cases had motility <50% after one hour, remaining 34 had motility >50%. Out of 120 cases of male infertility, 12 (10%) had Obesity and rest 108 (90%) had normal BMI. Out of 120 cases of male infertility, 8 (6.6%) were known Diabetics rest 112 (93.3%) had normal blood sugar levels. Out of 120 cases of male infertility, 36 (30%) had Erectile dysfunction and rest 84 (70%) were normal.Conclusions: The study concluded that Erectile dysfunction was the most common cause of male infertility. Varicoceles and small sized testes were the most common clinical abnormalities seen in infertile males. Smoking, Alcohol and Tobacco use were frequently associated with most infertile males.
The Effect of Comorbidity on Glycemic Control and Systolic Blood Pressure in Type 2 Diabetes: A Cohort Study with 5 Year Follow-Up in Primary Care

Aims To explore the longitudinal effect of chronic comorbid diseases on glycemic control (HbA1C) and systolic blood pressure (SBP) in type 2 diabetes patients. Methods In a representative primary care cohort of patients with newly diagnosed type 2 diabetes in The Netherlands (n = 610), we tested differences in the five year trend of HbA1C and SBP according to comorbidity profiles. In a mixed model analysis technique we corrected for relevant covariates. Influence of comorbidity (a chronic disease already present when diabetes was diagnosed) was tested as total number of comorbid diseases, and as presence of specific disease groups, i.e. cardiovascular, mental, and musculoskeletal disease, malignancies, and COPD. In subgroup effect analyses we tested if potential differences were modified by age, sex, socioeconomic status, and BMI. Results The number of comorbid diseases significantly influenced the SBP trend, with highest values after five years for diabetes patients without comorbidity (p = 0.005). The number of diseases did not influence the HbA1C trend (p = 0.075). Comorbid musculoskeletal disease resulted in lower HbA1C at the time of diabetes diagnosis, but in higher values after five years (p = 0.044). Patients with cardiovascular diseases had sustained elevated levels of SBP (p = 0.014). Effect modification by socioeconomic status was observed in some comorbidity subgroups. Conclusions Presence of comorbidity in type 2 diabetes patients affected the long-term course of HbA1C and SBP in this primary care cohort. Numbers and types of comorbidity showed differential effects: not the simple sum of diseases, but specific types of comorbid disease had a negative influence on long-term diabetes control parameters. The complex interactions between comorbidity, diabetes control and effect modifiers require further investigation and may help to personalize treatment goals.
Frequencies of dynamic obstructions of the upper respiratory tract in 135 Thoroughbreds during on-board exercise endoscopy

The frequencies of dynamic obstructions in thoroughbreds were investigated by performing on-board exercise endoscopy in 135 horses. 17 of these horses showed abnormal respiratory noise only and 35 solely poor performance. In 39 cases, both was reported. In addition, 44 horses underwent endoscopy without any clinical signs. In all of 56 horses that exhibited an audible abnormal respiratory noise, an obstruction of the upper respiratory tract was present. Overall, dynamic upper airway obstructions were detected in 72.6% (98/135). The most commonly diagnosed obstruction was axial deviation of the aryepiglottic fold (ADAF) in 55.1% of horses (54/98). 24.4% (24/98) showed palatal instability (PI), 30.6% (30/98) dorsal displacement of the soft palate (DDSP) and 11.2% (11/98) arytenoid cartilage collapse (ACC). Furthermore, 53.1% (52/98) of horses had abnormalities in the area of the vocal folds. Of these horses, 13 had unilateral or bilateral vocal cord collapse (VCC) and 8 displayed vibration of the vocal cords. 31 horses showed axial deviation in the area of the caudal vocal fold (ADPV) as a sole abnormality. By the new description of these ADPV, the origin of the abnormal respiratory noise in a further proportion of horses could be explained. Including ADPV, an obstruction of the upper airways was observed in all horses (100%) with specified abnormal respiratory noise. If only horses with long or continuous (>8sec) DDSP were taken into account, abnormal respiratory noise was audible in 93.3% and poor performance was present in 73.3%. It can thus be assumed that horses with DDSP requiring treatment are clinically apparent either with abnormal respiratory noise or poor performance. Furthermore, it was demonstrated, that in 52.3% of horses without poor performance or abnormal respiratory noise an dynamic upper airway obstruction was identified.
Natural Course of Perihemorrhagic Edema After Intracerebral Hemorrhage

Background and Purpose—There is only limited knowledge on the time course of perihemorrhagic edema (PHE) after intracerebral hemorrhage (ICH). We aimed to investigate the chronological PHE course and its relation to in-hospital mortality in a large retrospective ICH cohort. Methods—Patients with supratentorial ICH treated at our institution between 2006 and 2009, who had received at least 3 CT scans in the course of conservative treatment, were included in the present analysis. PHE at Days 1, 2, 3, 4 to 6, 7 to 11, 12 to 16, 17 to 21, and >22 was assessed using a threshold based semiautomatic volumetric algorithm. A chart review was performed to achieve data on duration of stay, ventilation, treatment with external ventricular drains, and in-hospital mortality. Results—Two hundred nineteen patients aged 69.9±10.5 years with deep (n=103) or lobar (n=116) ICH were included in the study. Mean ICH volume was 35.7±31.5 mL. Mean absolute PHE volume significantly increased from initially 32.6±29.9 mL to 63.7±46.