Kornimate/medical-research-clean huggingface dataset:
whole genome trio sequencing as a standard routine test in patients with rare diseases - "genome first approach"

Conditions: Rare Diseases; Genetic Predisposition

Summary: the genome first approach project will enroll patients (n = 450) and their healthy parents with unclear molecular cause of the disease, suspected genetic cause of the disease and the healthy parents of those affected for trio analysis (n in total 1350).

in the genome first approach (monocentric, prospective, open-label diagnostic) project, patients with molecularly undiagnosed diseases will diagnostically be analyzed by whole genome sequencing (wgs)-trio analysis. the following questions will be leading the project: primary: • efficacy of wgs trio analysis in different clinical indications secondary: * systematically benchmark wgs analysis to detect genetic variations compared to wes and single nucleotide polymorphism (snp) array analysis, * expand the analysis from coding single-nucleotide variants (snvs) to regulatory mutations, structural variants (svs), and low complexity regions, * validate the efficacy of clinical genome trio sequencing in a routine diagnostic setting, * analyse whether 42x coverage has the potential to discover mosaicism as disease causing mechanism, * further develop algorithms for integrative analyses of trio-wgs data with ribonucleic acid- sequencing (rna-seq), * identify de novo alterations and novel disease mechanisms, * gain fundamental new insights into disease mechanisms and cellular biology, * combine wgs with further omics methods to improve genetic diagnostics of future rare disease patients, and * explore overall financial costs and time to report conclusive data to the patients of the trio-wgs approach compared to traditional multistep diagnostic approaches using single-gene, panel, whole-exome sequencing (wes) and chromosomal microarray (cma) (snp array, array-based comparative genomic hybridization (arraycgh)) analysis. in addition, healthy parents of the subjects will be included in the project to perform parent-child (trio) analyzes.

Eligibility criteria:
inclusion criteria: * unclear molecular cause of the disease * suspected genetic cause of the disease * healthy parents of those affected for trio analysis cohort 1: iq \< 70 with and without malformations, syndromic and non-syndromic cohort 2: retinitis pigmentosa, achromatopsy, bardet-biedl syndrome, usher syndrome, congenital stationary night blindness, lca, macula degeneration, rod/ cone dystrophies, opticus atrophy cohort 3: rare paediatric solid cancers as melanoma, carcinoma of the gastrointestinal tract, tumours of the salivary gland and pancreatic tumors in children. exclusion criteria: cohort 1: toxic causes (drugs, infections) cohort 2: patients with non-genetic forms of blindness cohort 3: adult cancer, blood cancer * missing informed consent of the patient/ legal guardian * missing samples of both parents * previous wes or panel analysis-

Keywords: rare diseases genetic predisposition whole-exome sequencing wgs-trio analysis whole genome sequencing (wgs)
a study to compare the experiences of taking daily growth hormone injections to weekly ngenla in children with low levels of growth hormone

Conditions: Pediatric Growth Hormone Deficiency

Summary: the purpose of this study is to learn about: * how children stick to taking their injections * their experience with the study medicines (ngenla and daily growth hormone) prescribed to children with low levels of growth hormone. this study is seeking participants who: * are being treated or are ready to start treatment with daily growth hormone or ngenla. * use a sharps bin to collect used needles. the study medicines will be given as per regular care agreed with the doctor. the study will compare participant experiences to help us see: - the difference in how the participants stick to taking their daily growth hormone injections compared to participants using once weekly ngenla. participants will take part in this study for up to 14 months. during this time, they will have 3 study visits at the study clinic. the participants will use the healthbeacon™ smart sharps bin for collecting the used needles or injections.

this multicenter, international, longitudinal, prospective, site-based, low-interventional study aims to evaluate and monitor treatment experience, defined by treatment adherence and persistence, in children aged 3-16 years old with a diagnosis of pediatric growth hormone deficiency (pghd), receiving either daily growth hormone (dgh) treatment or once weekly ngenla. the study is planned to be conducted in a total of 50 participating sites distributed across belgium, canada, france, italy, luxembourg, spain, uk, and us. data on treatment adherence and persistence will be collected in real-time over a period of 12 months using the healthbeacon™ smart sharps bin™ as a treatment monitoring device. additional data, including demographic and clinical characteristics, will be collected at three timepoints, in line with the routine care in each participating site and/or country, over a maximum period of 14 months. approximately 400 participants will be enrolled in the study (approximately 200 participants prescribed dgh injections and approximately 200 prescribed ngenla).

Eligibility criteria:
inclusion criteria: 1. children of any sex aged 3-16 years at baseline 2. children that have received a diagnosis of pghd requiring gh injections. 3. children that are currently being treated (dgh/ngenla) or are treatment naïve but ready to start treatment. 4. those who currently use a sharps bin to collect used needles \[as per normal standard of care (soc)\]. exclusion criteria: 1. children with psychosocial dwarfism. 2. children born small for gestational age (sga) 3. children with chromosomal abnormalities 4. children with other causes of short stature, such as uncontrolled primary hypothyroidism or rickets. 5. children with a history of cancer. 7. children with other acute medical or psychiatric condition

Keywords: adherence pediatric ngenla growth hormone growth hormone deficiency daily growth hormone smart bin treatment experience
adapting dialectical behavior therapy for children in residential care

Conditions: Childhood Aggression

Summary: i: conduct pilot randomized clinical trial of dialectical behavior therapy for children (dbt-c) in residential as compared with treatment-as-usual (tau) (60 children in dbt-c and 60 children in the comparison condition). ii: finalize therapist training manuals and educational materials to guide selection, training, and supervision of treatment providers.

specific aim 1: examine feasibility of dbt-c by evaluating response rate in treatment attendance, treatment satisfaction, and any differences in these rates by groups. hypothesis 1: dbt-c will be equivalent to tau in attendance rate and will have significantly greater treatment satisfaction rating by subjects, as well as by therapists and milieu staff. specific aim 2: examine efficacy of dbt-c as compared to tau in reducing internalizing and externalizing symptoms. hypothesis 2: children in dbt-c condition as compared to tau will have significantly fewer internalizing and externalizing symptoms. specific aim 3: examine efficacy of dbt-c in improving adaptive coping, emotion regulation, risk taking, and social skills, and reducing depression. hypothesis 3: children in dbt-c training condition as compared to tau will have significantly greater improvement in adaptive coping skills, emotion regulation, risk taking and impulsivity and social skills, and reducing depressive symptoms. specific aim 4: examine efficacy of dbt-c in reducing the frequency of critical incidents. hypothesis 4: children in dbt-c condition as compared to tau will have significantly fewer critical incidents, including psychiatric hospitalization, emergency room visits, total number of days inpatient, suicidal ideations and attempts, self-harm behaviors, sexual acting out, running away, stealing, police involvement, etc.

Eligibility criteria:
inclusion criteria: * age between 6 years 0 months and 12 years 11 months; * male; * in residential care at green chimneys; * projected length of stay is at least 8 months. exclusion criteria: * pervasive developmental disorder; * psychotic disorder; * mental retardation; (all as per psychiatric evaluation at green chimneys); * in care or custody of the department of social services (dss); * caregivers do not speak english.

Keywords: dbt, child, emotion regulation, behavior problems
effect of polyphenol-rich dark chocolate on body weight in overweight and obese adults

Conditions: Body Weight

Summary: the aim of this study is to investigate if dark chocolate rich in polyphenols decreases body weight/ body fat in the overweight and obese adult population.

polyphenols are phytochemicals widely available in plants, and may have several favourable effects on health. dark chocolate (dc) is one of the highest sources of polyphenols in foods. animal and in vitro studies have demonstrated that cocoa and dark chocolate may exert anti-obesity effects mainly due to the polyphenol effect on glucose and fatty acid metabolism. human studies have showed that regular chocolate eaters have a lower body weight compared to non regular eaters, and that dc promotes satiety and reduces cravings. the aim of this pilot study is to investigate the effect of polyphenol-rich dc on body weight in the overweight and obese adult population, when incorporated into a non-restricted diet. twenty-eight apparently healthy volunteers will be recruited. participants will randomly receive 20g daily of one of the two different types of dc: placebo dc (low in polyphenols) or dc rich in polyphenols (500mg) for a period of twelve weeks. participants will be asked to make three appointments and one follow-up appointment to the university clinical lab. anthropometric measurements (height, weight, waist circumference, body fat percentage) will be taken during each visit. compliance will be defined by the intake of 85 % or more of the chocolate weekly, and will be tested by the measure of total polyphenols in a 24-hour urine sample before, during and at the end of the intervention. to monitor any fluctuations in the participants' diet or physical activity during the study period, a three-day diet diary, a food frequency questionnaire assessment for polyphenol intake and a physical activity questionnaire will be collected before the start of the study and every four weeks. a follow-up appointment (four weeks after the end of intervention) will check if any differences in anthropometric measures have been maintained. data will be analysed with an ancova with time (pre- and post-) and treatment (dc and placebo) as between-subject factor. this study will have novel findings and will be the basis for a future larger trial.

Eligibility criteria:
inclusion criteria: * healthy adults * bmi between 25-35 * males and females * age: 18-65 years exclusion criteria: * participants with cardiovascular diseases, hypertension or diabetes * participants taking any medications that affect insulin, cholesterol, triglycerides or blood pressure * participants who recently participated or are currently on a weight management program * participants with regular consumption of cocoa or dc (\> 1 serving/week)
tecovirimat intravenous treatment for orthopox virus exposure

Conditions: Orthopox Virus Infection

Summary: * to provide a therapeutic option for patients not able to take the oral formulation of tpoxx (e.g., cannot swallow, vomiting) and who have confirmed or suspected (based on clinical signs and symptoms with known exposure while laboratory confirmation may be pending) orthopox virus infections or who have a significant vaccinia adverse reaction (as defined in the protocol) resulting from vaccinia vaccination, secondary transmission, or other exposure; * to collect data on the safety of tpoxx iv (tecovirimat injection, 10 mg/ml).


Eligibility criteria:
inclusion criteria: 1. have a confirmed or suspected (based on clinical signs and symptoms with known or suspected exposure and/or positive or pending laboratory confirmation) orthopox virus infection. note: patients with a negative orthopox virus diagnostic test but with epidemiological and clinical evidence of an orthopox viral infection, especially those with evidence of clinical disease progression, may be included. primary/treating physician may consult with sponsor's subject matter expert; or have developed a significant vaccinia adverse reaction (e.g., eczema vaccinatum, progressive vaccinia, generalized vaccinia that is severe or persistent, and select cases of inadvertent inoculation due to severe pain related to mucosal involvement, ocular involvement) resulting from vaccination, secondary transmission, or other exposure; 2. be dod-affiliated personnel (including active and reserve component service members, us civilian employees, contractors, other us personnel, and dependents, as well as allied military forces and local nationals) who have been granted access to the medical facility; 3. unable to take the oral formulation of tpoxx (e.g., unable to swallow capsules or take medication powder dissolved in soft food or liquid, vomiting); 4. is available for clinical follow-up for duration of the treatment and follow-up period; 5. females of childbearing potential must use a highly effective method of contraception during treatment and for 30 days after the last dose of drug. male patients with a female partner of childbearing potential must use an acceptable method of contraception and refrain from donating sperm during treatment and for 30 days after the last dose. exclusion criteria: 1. hypersensitivity to tecovirimat; 2. unable or unwilling to cooperate with the requirements of the protocol; 3. breastfeeding women: nursing mothers will be counseled that tecovirimat has not been studied in breast-feeding women. women who choose to continue breastfeeding will not be enrolled in this protocol. however, if a patient elects to stop breastfeeding for the duration of the study until 30 days after the last dose of the tpoxx iv, she may be enrolled.
does higher (100% oxygen) versus lower (21% oxygen) during cc+si during cpr of asphyxiated newborns improve time to rosc

Conditions: Heart; Arrest, Newborn; Birth Asphyxia; Bradycardia Neonatal

Summary: when newborn babies are born without a heartbeat the clinical team has to provide breathing and chest compressions (what is call cardiopulmonary resuscitation) to the newborn baby. cardiopulmonary resuscitation is an infrequent event in newborn babies (\~1% of all deliveries), approximately one million newborn babies die annually due to lack of oxygen at birth causing being born without a heartbeat. outcome studies of newborn babies receiving cardiopulmonary resuscitation in the delivery room have reported high rates of death and neurological impairment. this puts a heavy burden on health resources since these infants require frequent hospital re-admission and long-term care. the poor prognosis raises questions as improve cardiopulmonary resuscitation methods and specifically adapt them to newborn babies to improve outcomes. currently a 3:1 ratio, which equals 3 chest compressions to one rescue breath to resuscitate a newborn baby. this means that chest compressions are stopped after every 3rd compression to give one rescue breath. the investigators believe that this interruption of chest compressions is bad for the newborn baby and that chest compressions should be continued without interruption while rescue breaths are given continuously. the investigators believe that this approach will allow us to reduce death and long-term burdens in newborn babies born without a heartbeat. furthermore, it is not known if rescue breaths given with 100% oxygen or 21% oxygen (room air) is better for newborn babies. using continuous chest compressions and rescue breaths without interruptions, this study will compare 21% with 100% oxygen.


Eligibility criteria:
inclusion criteria: * term infants requiring chest compressions in the delivery room * preterm infants \>28 weeks' gestation requiring chest compressions in the delivery room exclusion criteria: * infants with congenital abnormality * infants with congenital diaphragmatic hernia or congenital heart disease * infants who's parents refused to give consent to this study

Keywords: chest compression newborn infant sustained inflation
newly diagnosed with inflammatory arthritis - a self-management intervention (nisma)

Conditions: Feasibility

Summary: even though medical treatment has improved within the last 10-15 years, patients with inflammatory arthritis (ia) still experience reduced quality of life, depression, anxiety, changes in family roles, work life, and social relationships. particularly the newly diagnosed, require regular consultations and available support from health professionals, to be able to handle emotional, social, and physiological challenges. the hypothesis is that a self-management intervention can improve patients' ability to monitor their arthritis and respond to symptoms, reduce the risk of co-morbidities, and improve adherence. and also, that they can develop cognitive, behavioral, and emotional strategies to manage life with arthritis. there is a lack of disease-specific evidence, in integrated interventions with multiple components targeting patients with a newly diagnosed ia. in a previous study, the investigators developed a self-management intervention, and now wish to test it in a randomized feasibility study.

rationale for nisma project the hypothesis is that a self-management intervention can help patients develop behavioral and emotional strategies to manage life with arthritis. there a lack of disease-specific evidence, in integrated interventions with multiple components targeting patients with a newly diagnosed ia. therefore, the investigators wish to develop a self-management intervention. aim the overall aim of this study is to determine whether a full-scale randomized controlled trial, which aims to increase self-management in patients with newly diagnosed ia, is possible. the investigators wish to identify methodological, clinical, and procedural uncertainties in delivering a self-management intervention. furthermore, to investigate outcomes related to recruitment, including adherence, retention, accrual rate, characteristics of the sample, and reliable recruitment methods. design this feasibility study is designed as a randomized controlled feasibility trial (allocation ratio 1:1) to assess the proposed method in the definitive rct. overall setting the intervention will take place at the center for rheumatology and spine diseases, rigshospitalet, denmark.

Eligibility criteria:
inclusion criteria: * adult persons (≥18 years) * diagnosed with one of the following diagnoses: rheumatoid arthritis (icd10 diagnoses: m05.3, m05.9, m05.8, m06.9), spondyloarthritis (icd10 diagnoses: m45.9, m46.1, m46.8, m46.9) or psoriatic arthritis (icd10 diagnoses: m073.a, m073.b), within the last 6 months. exclusion criteria: * insufficient language skills to discuss the topics in the intervention in danish * in chemotherapy treatment for malignancies
safety and effectiveness of s-adenosyl-l-methionine (same) for the treatment of major depression

Conditions: Depression

Summary: the purpose of this study is to determine the safety and effectiveness of s-adenosyl-l-methionine (same) in treating major depression.

same is a substance that is naturally produced by the body and is also sold as an over-the-counter drug. although same has not yet been approved for treating depression, evidence suggests that it has antidepressant properties. this study will determine whether same is safe and effective in treating major depression. this study will last 24 weeks. participants will be randomly assigned to receive either the antidepressant escitalopram, same, or placebo for 12 weeks. participants who respond to treatment at the end of 12 weeks will stay on their regimen for an additional 12 weeks. participants who do not respond to treatment will enter an open treatment phase where they will receive same and escitalopram for 12 more weeks. depression scales and self-report questionnaires will be used to assess participants. all participants will receive 3 months of follow-up care, including free medication and clinic visits as necessary.

Eligibility criteria:
inclusion criteria: * diagnosis of major depression * score of 25 or higher on the inventory of depressive symptomatology (ids-c) scale * score of higher than 2 on the clinical global impression improvement (cgi) scale * willing to use acceptable methods of contraception exclusion criteria: * suicidal or homicidal * unstable illness, including cardiovascular, hepatic, renal, respiratory, endocrine, neurological, or hematological disease. * any of the following mental conditions: organic mental disorders; schizophrenia; delusional disorder; psychotic disorders; bipolar disorder; recent bereavement; severe borderline or antisocial personality disorder; panic disorder; or obsessive compulsive disorder * substance abuse, including alcohol abuse, within 6 months prior to study entry * uncontrolled seizure disorder, or a seizure disorder controlled with psychotropic anticonvulsants * psychotic features * current use of other psychotropic drugs * hypothyroidism * have taken 6 weeks or more of either escitalopram or same during the current depressive episode * previous intolerance of same or escitalopram * investigational psychotropic drugs within 1 year prior to study entry * have received two or more antidepressant therapies of adequate doses and duration and failed to respond * have received depression-focused psychotherapy * bleeding tissue disorder, low platelet counts, a history of gi bleeding, or use of medications that alter bleeding risk * long-term aspirin use * pregnancy

Keywords: depression antidepressive agents complementary therapies