Kornimate/medical-research-clean huggingface dataset:
icages-guided precision therapy for cancers in contrast to standard care or ihc-guided theray

Conditions: Lung Cancer; Gene Abnormality; Gene Product Sequence Variation; Cancer

Summary: this study prospectively evaluates whether the use of icages (integrated cancer genome score) tool in guiding the treatment of advanced cancers is superior to current standard care or ihc-guided therapy in progress free survival (pfs),overall survival (os),and improvement of life quality.

cancer is a fatal disease caused by the accumulation of various oncogene and tumor suppressor gene mutations. studies of high-throughput sequencing for patients who suffered from cancer has found that different mutations play a different role in the occurrence and development of different cancers. several gene panels already exist to help identify mutations in a few genes that may have corresponding fda-approved drugs or drugs under clinical trials. however, given whole-genome/exome sequencing data, the suitable clinical analysis tool to analyze individualized cancer-related gene mutations, and recommend the most appropriate targeted treatment options among hundreds of possible drugs therapy is absent currently. the recently proposed icages is a precise biomedical informatics analysis tool, which could help increase the accuracy of cancer driver gene detection and prioritization, bridge the gap between personal cancer genomic data and prior cancer research knowledge,and facilitate cancer molecular diagnosis as well as personalized precision therapy. ihc detection of multiple molecules such as egfr, her2-3, trop3, nectin4, met, b7-h3-4, b1-h7, claudin18.2, fgfr1-4, mesothelin, ror1, bcma, axl, tf, frα, cd70, pparα, hif-2α, ret, ros1, ntrk, cdk4/6, flt3, ezh2 are also scheduled for appropriate targeted therapy and comparison if available.

Eligibility criteria:
inclusion criteria: * pathological and clinical diagnosis of recurrence / metastatic lung cancer or other advanced cancers. * there are pacs images available at the second affiliated hospital of guangzhou medical university and the collaborated hospitals. * the patient is informed consent and signed a written consent. exclusion criteria: * age \> 70 or \<18 years old. * previous history of malignant tumors. * pregnant or lactating female patients. * any serious concomitant disease that is expected to have an adverse effect on prognosis, including the heart disease that treatment is required, unsatisfactory controlled diabetes and psychiatric disorders.

Keywords: lung cancer icages gene mutation precision medicine advanced cancers ihc targeted therapy
an open-label safety, tolerability, and dose-range finding study of nusinersen (isis 396443) in participants with spinal muscular atrophy (sma)

Conditions: Spinal Muscular Atrophy

Summary: this objectives of this study are to evaluate the safety, tolerability, and pharmacokinetics of a single dose of nusinersen (isis 396443) administered intrathecally to participants with spinal muscular atrophy (sma).

this study was conducted and the protocol was registered by ionis pharmaceuticals, inc. in august 2016, sponsorship of the trial was transferred to biogen.

Eligibility criteria:
key inclusion criteria: * documented survival motor neuron1 (smn1) homozygous gene deletion * clinical signs attributable to spinal muscular atrophy (sma) * able to complete all study procedures, measurements and visits and parent/participant has adequately supportive psychosocial circumstances, in the opinion of the investigator * estimated life expectancy \> 2 years from screening * meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is planned for study procedure key exclusion criteria: * respiratory insufficiency defined by the need for invasive or non-invasive ventilation during a 24 hour period * presence of a gastric feeding tube * previous scoliosis surgery or scoliosis surgery planned during the duration of the study that would interfere with the lumbar puncture (lp) injection procedure * hospitalization for surgery or pulmonary event within the last 2 months or planned during the study * presence of an untreated or inadequately treated active infection requiring systemic antiviral or antimicrobial therapy * history of brain or spinal cord disease that would interfere with lp procedures or cerebrospinal fluid (csf) circulation * presence of an implanted shunt for the draining of csf or an implanted central nervous system (cns) catheter * history of bacterial meningitis * clinically significant abnormalities in hematology or clinical chemistry parameters * treatment with another investigational drug, biological agent, or device within 1-month of screening or 5 half-lives of study agent whichever is longer. any history of gene therapy or cell transplantation * ongoing medical condition that would interfere with the conduct and assessments of the study. examples are medical disability (e.g. wasting or cachexia, severe anemia, etc.) that would interfere with the assessment of safety or would compromised the ability of the participant to undergo study procedures note: other protocol defined inclusion/exclusion criteria may apply.

Keywords: spinal muscular atrophy sma smn smnrx isis-smnrx isis-smn rx isis 396443 ionis-smnrx ionis-smn rx spinraza
vaporous hyperoxia therapy (vht) in the treatment of foot wounds

Conditions: Neuropathic Foot Ulcer; Foot Ulcer

Summary: the purpose of this study is to evaluate the effectiveness of vaporous hyperoxia therapy (vht), previously named misty (wts-1000) for the treatment of chronic foot ulcers.

the vaporox vht1 study is a single arm study evaluating the efficacy of vaporous hyperoxia therapy (vht), previously named misty (wts-1000), as an adjunctive therapy for the treatment of chronic foot ulcers.

Eligibility criteria:
inclusion criteria: * diabetic, arterial, and venous foot ulcers as well as decubitus ulcers * university of texas health science center classification: grade 0, 1, and 2 exclusion criteria: * ulcers above the medial and lateral malleoli * etiology of cancer/neoplastic * etiology of collagen vascular disease * etiology of gangrene * etiology of osteomyelitis (grade 3) * etiology of thermal burns * etiology of radiation injury * pregnancy * acute skin conditions * inadequate perfusion to support treatment * wounds where the end cannot be probed * wounds covered with petroleum based dressing * non-compliant patients

Keywords: diabetic foot leg ulcer skin ulcer
clinical performance of the gynecare prolift + m* pelvic floor repair system as a device for pelvic organ prolapse

Conditions: Cystocele; Rectocele; Enterocele

Summary: the purpose of this study is to evaluate the clinical performance of the prolift system with a new lighter-weight mesh in repair of vaginal prolapse.

vaginal prolapse (a feeling of bulge in the vagina) may cause some distressing symptoms such as loss of control of the bowel or bladder, and may also cause problems with women's sex life. there are a number of different surgical procedures which are used to repair prolapse. sometimes a mesh is placed in the pelvis to support the weakened tissues. there is a lot of research going on to find the most suitable type of mesh to repair vaginal prolapse. the gynecare prolift + m\* pelvic floor repair system is similar to a mesh already used for this procedure called ultrapro\*, but is lighter in weight. currently, ultrapro\* is only approved for use in hernia repair and is not licensed for gynecological procedures. this study will be the first clinical investigation of this mesh in vaginal prolapse.

Eligibility criteria:
inclusion criteria: * candidates with symptomatic pelvic organ prolapse of ics pop-q stage iii or iv, suitable for surgical repair. perineal repair, vaginal hysterectomy and/or mid urethral sling procedures for incontinence may be performed concurrently. * age \> or = 18 years. * agrees to participate in the study, including completion of all study-related procedures, evaluations and questionnaires, and documents this agreement by signing the ethics committee / irb approved informed consent. exclusion criteria: * additional surgical intervention for pop repair concurrent to the gynecare prolift+m procedure (e.g. paravaginal repair, sacrocolpopexy, colporrhaphy in a non-gynecare prolift+m treated compartment). * previous repair of pelvic organ prolapse involving insertion of mesh. * previous hysterectomy within 6 months of scheduled surgery. * experimental drug or experimental medical device within 3 months prior to the planned procedure. * active genital, urinary or systemic infection at the time of the surgical procedure. surgery may be delayed in such subjects until the infection is cleared. * coagulation disorder or on therapeutic anticoagulant therapy at the time of surgery. * history of any pelvic radiation therapy. * history of chemotherapy within 6 months of the planned procedure. * systemic disease known to affect bladder or bowel function (e.g. parkinson's disease, multiple sclerosis, spina bifida, spinal cord injury or trauma). * current evaluation or treatment for chronic pelvic pain (e.g. interstitial cystitis, endometriosis, coccydynia, vulvodynia). * nursing or pregnant or intends future pregnancy. * in the investigator's opinion, any medical condition or psychiatric illness that could potentially be life threatening or affect their ability to complete the study visits according to this protocol.

Keywords: anterior vaginal prolapse (medial, lateral,apical cystocele) posterior vaginal prolapse (rectocele and/or enterocele) vault prolapse (enterocele, uterine/vaginal vault prolapse)
synaptic plasticity and cognitive function in rasopathies

Conditions: Impaired Synaptic Plasticity; Impaired Cognition

Summary: the project is targeting cognitive impairment, one of the main health problems of patients with ras pathway disorders. the aim of this study is to translate findings of animal studies to humans. this has been done by the applicants successfully for lovastatin in nf1. this result will be transferred to patients with noonan syndrome. lamotrigine is most likely a more effective and promising substance improving synaptic plasticity and consecutive cognitive function. it is expected that both substances are improving synaptic plasticity as well as alertness and changes in alertness may be a precondition for improvement of cognition.


Eligibility criteria:
inclusion criteria: 1. group 1: ns, group 2: nf1 (both genetically assured) 2. age ≥16 years 3. the adolescent (≥16) and legal guardian who are capable to give their consent and understand the aim and rationale of the study. in case of doubts, an independent medical practitioner will evaluate the capacity to consent. 4. signed informed consent if ≥ 16 years and legal guardian. 5. persons who are ≥ 18 years old and capable to give their consent and understand the aim and rationale of the study. in case of doubts, an independent medical practitioner will evaluate the capacity to consent. 6. signed informed consent if ≥ 18 years. 7. male participants and female participants who are not capable of bearing children or who use a method of contraception that is medically approved by the health authority of the respective country. exclusion criteria: 1. epilepsy 2. medication with known cns effects 3. severe mental retardation 4. side effects during previous medication with and contraindications for ltg and/or lov and/or tms 5. psychiatric diseases 6. previous history of allergic reactions with ltg and lov medications 7. potentially unreliable patients 8. patients who are not suitable for the study in the opinion of the investigator 9. pregnancy (incl. positive urine pregnancy test) 10. persons who are incapable of giving consent or do not understand the aim or rationale of the study.

Keywords: rasopathies, neurofibromatosis type 1, noonan syndrome, synaptic plasticity, transcranial magnetic stimulation
oab and the microbiome

Conditions: Overactive Bladder; Urgency-frequency Syndrome

Summary: to determine differences in the urinary microbiomes, identified by polymerase change reaction (pcr) (utip™), of female patients with urgency and frequency syndrome with or without pelvic pain (group a) compared to female controls without symptoms of lower urinary tract symptoms (luts) (group b).


Eligibility criteria:
inclusion criteria: * 18 y/o-90 y/o * able to consent * group a only: urgency and frequency syndrome or oab only. udi-6 answer of "moderately" to "quite a bit" on questions 1 or 2. * group b only: urinary distress inventory 6 (udi-6) answer "not at all" or "somewhat" for questions 1 or 2. exclusion criteria: * pregnant * pelvic radiation * urinary retention (\>200 ml) * renal calculi * recurrent urinary tract infection (uti) (2 in 6 months), or * current uti * immunosuppressed or radiation history * neurologic disorder
gene expression profiling of metastatic breast cancer predict the therapeutic response to chemotherapy

Conditions: Breast Neoplasms; Neoplasm Metastasis

Summary: the investigators want to develop a gene expression profile the for prediction the chemotherapeutic response of patients with metastatic breast cancer.

1. metastatic breast cancer tissue is obtained from core needle biopsies pretreatment and is flash frozen and stored at -70℃ until processing. 2. after patients received docetaxel combination thiotepa for two cycles, response is assessed using response evaluation criteria in solid tumor group (recist) guidelines. degree of response is used to divide the cancers into two groups-sensitive and resistant tumours. 3. the gene expression in metastatic breast cancer tissue sample is detected by microarray to screen gene markers that are differently expressed between groups 4. statistical analysis is performed using unsupervised hierarchical cluster.

Eligibility criteria:
inclusion criteria: * patients should be histologically confirmed with metastatic breast cancer; * patients who had completed the planned chemotherapy regimen with no major protocol violation; * an eastern cooperative oncology group (ecog) performance status of 0-2; * at least one measurable lesion; * normal cardiac, hepatic, renal and bone marrow functions; * life expectancy ≥3 months; * discontinuity of previous chemotherapy for a minimum of 4 weeks. exclusion criteria: * previous history of other malignancies; * previous surgery history on the needle biopsy organ; * central nervous system metastases; * serious or uncontrolled concurrent medical illness.

Keywords: metastatic breast neoplasms gene expression profiling drug therapy
erythrocyte ghost mediated retinal diagnosis

Conditions: Retinal Disease

Summary: instead of the usual procedure of injecting icg dye directly into an arm vein, now the dye can be placed inside of rbcs. when a small volume of the rbc's with the dye is injected into a person's arm, the individual rbcs can be seen as they flow through the retinal blood vessels.

capillary erythrocyte movement throughout the entire human macula can be observed routinely for periods up to 20 minutes by autologous re-injection of a small volume (about 1 ml) of indocyanine green (icg)-loaded erythrocytes, making possible for the first time quantification of blood flow in individual capillaries, including abnormal structures like choroidal neovascularization (cnv), and it makes possible characterization of vasomotion in ocular vasculatures.

Eligibility criteria:
inclusion criteria: 1. a male or female, of any race who is at least 40 years of age and has clinical signs of cnv or exudative manifestations of amd, has clinical signs of dr, or clinical signs of retinal occlusive disease. 2. patients with subfoveal, extrafoveal or juxtafoveal cnv, which is classic, minimally classic or occult and has dimensions less than 25.0 mm2 as measured on the sodium fluorescein angiogram (sfa). 3. patient with recurrent cnv, where previous treatment never involved the foveal avascular zone (faz). 4. analysis of highspeed icga must show one or more welldefined feeder vessel. 5. patient must have best corrected visual acuity based on the etdrs chart between 20/40 and 20/320 in the study eye. 6. patient must be willing, be able to comply with the protocol and provide informed consent. exclusion criteria: 1. cnv secondary to any cause other than amd or dr. 2. patient with significantly compromised visual acuity in the study eye due to concomitant ocular conditions. 3. patient participating in any other investigational drug study. 4. patient with significant liver disease or uremia. 5. patient with known adverse reaction to indocyanine green or iodine. 6. patient is pregnant or nursing.
amoxicillin and metronidazole in association with non-surgical therapy in aggressive periodontitis treatment

Conditions: Generalized Aggressive Periodontitis

Summary: this study is designed as a parallel, masked, randomized, placebo-controlled clinical trial to assess the clinical, microbiological, and immunological outcomes of scaling and root planning (srp) or full-mouth ultrasonic debridement (fmud) with am (amoxicillin + metronidazole) for the treatment of generalized aggressive periodontitis (gagp).

forty eight gagp patients were divided into 4 groups: the srp group (n = 12), which received srp plus placebo, and the srp+am group (n = 12), which received srp and 375mg amoxicillin plus 250 mg metronidazole for 7 days, the fmud group (n = 12), which received fmud plus placebo, and the fmud+am group (n = 12), which received fmud and 375mg amoxicillin plus 250 mg metronidazole for 7 days. the following clinical outcomes were tested: plaque and bleeding on probing indices, pocket probing depth (pd), relative gingival margin position (gmp), and relative clinical attachment level (cal). the total amount of porphyromonas gingivalis (pg), aggregatibacter actinomycetemcomitans (aa), tannerella forsythia (tf), and gingival crevicular fluid (gcf) concentration of interleukin (il)-10 and il-1b were also determined. all clinical, microbiological, and immunological parameters were assessed at baseline and at 3 and 6 months post-therapy. the anova/tukey test was used for statistical analysis (a = 5%).

Eligibility criteria:
inclusion criteria: * diagnosis of gagp; * presence of 20 teeth; * presence of teeth presenting pd\>5 mm with bleeding on probing (bop) and 2 teeth with pd\>7mm (including incisors and first molars, in addition to two other non-contiguous teeth between them); * good general health; * \<35 years of age. exclusion criteria: * were pregnant or lactating; * were suffering from any other systemic diseases (e.g., cardiovascular, diabetes); * received antimicrobials in the previous 3 months; * were taking long-term anti-inflammatory drugs; * received a course of periodontal treatment within the last 6 months; * smoked

Keywords: aggressive periodontitis anti-infective agents debridement randomized clinical trial ultrasonic
ifosfamide and doxorubicin in patients with refractory nasopharyngeal carcinoma

Conditions: Refractory Nasopharyngeal Carcinoma

Summary: this research is to test the effectiveness and toxicity of both ifosfamide and doxorubicin. it also aims to explore the relationship between ebv dna and clinical response in patients with advanced naso-pharyngeal cancer which has been previously treated with chemotherapy.

nasopharyngeal cancer (npc) is one of the common cancer in southeast asia. in this region npc is associated with epstein barr virus (ebv) chronic infection with ebv dna identifiable in almost all the npc tumors and patient's serum at the time of diagnosis. chinese, especially cantonese has the highest incidence. only about 30% of patients presents early disease and has a good treatment outcome (80% cure for stage i disease and 70% for stage ii by radiation). this research is to test the effectiveness and toxicity of both ifosfamide and doxorubicin. it also aims to explore the relationship between ebv dna and clinical response in patients with advanced naso-pharyngeal cancer which has been previously treated with chemotherapy. investigators believe ebv infection is necessary to cause npc and that ebv dna levels in the blood may directly relate to the total size of the tumor. because npc patients in this situation have a poor outlook, we design this study to evaluate the combination of ifosfamide and doxorubicin for further treatment. while this combination of medicines has been used in many other forms of cancer, it has not been tested in patients with npc.

Eligibility criteria:
inclusion criteria: * histological diagnosis of npc * age \> 18 years old * measurable metastatic or recurrent disease (s) * received one prior chemotherapy regimen for metastatic or recurrent npc which relapsed or became refractory before entry. * ecog ps 0, 1 or 2 * wbc \> 3,500/ul and anc \> 1,500/ul platelet \> 100,000/ul creatinine - within normal limits sgot \< 3 x unl bilirubin \< 2.0 mg/dl * ejection fraction \> 45% and no history of myocardial infarction or congestive heart failure in the last 6 months. no history of cardiac ventricular arrythmia or ventricle tachycardia, or uncontrolled atrial fibrillation or supraventricular tachycardia with hemodynamic compromising status. * random blood glucose level \< 250 mg * signed informed consent exclusion criteria: * received more than one prior chemotherapy for metastatic or recurrent disease * ejection fraction \< 45% * wbc \ 3 x unl or bilirubin \> 2.0 mg/dl or creatinine \> unl * ecog ps \> 3 * hx of myocardial infarction within last 6 months * random blood glucose level less than or equal 250 mg
pilot study in multi-coil repetitive transcranial magnetic stimulation (rtms) for treatment resistant depression

Conditions: Major Depressive Disorder

Summary: the purpose of this study is to assess the efficacy of a deep shaped-field repetitive transcranial magnetic stimulation (dsf-rtms) system in the treatment of depression.


Eligibility criteria:
inclusion criteria: * major depressive disorder (mdd) * mild to moderate level of resistance or intolerance to antidepressant treatment in the current episode. * will not become pregnant during study. exclusion criteria: * seizure disorder. * history of brain injury or active cns disease. * metal implants on or in brain, spinal cord, ear, eye or heart. * current use of proconvulsant medications (e.g., bupropion). * other significant psychiatric disorder. * substance use disorder (not including caffeine or nicotine). * 7 or more failed treatment attempts for depression in one's lifetime. * have failed to clinically remit to an adequate trial of ect or tms.

Keywords: depression mdd transcranial magnetic stimulation depressive disorder tms
evaluation of cold forcep and cold snare polypectomy for polyps less than or equal to 3mm in size during colonoscopy

Conditions: Colo-rectal Cancer; Polyp of Colon; Adenomatous Polyp of Colon

Summary: the focus of the study is to evaluate impact of cold forcep and cold snare in achieving complete resection during polypectomy of polyps \<=3mm during colonoscopy.

the details of the proposed study are as follows: 1. experimental group: using cold forceps for polyps \<=3mm of the colon 2. control group: using cold snare for polyps \<=3mm of the colon 3. methods: 1. colonoscopy will be performed in the same standard of care manner as if no study was taking place. 2. if polyps \<=3mm are identified, the endoscopist is randomized to performing polypectomy with cold forcep or cold snare. 3. after removal of the polypectomy, two biopsies are performed at the margin of the polypectomy site to identify residual lesion. 4. the polyp as well as well as the two biopsies are reviewed by a pathologist.

Eligibility criteria:
inclusion criteria: * patients 18 years or older * polyps \<=3mm exclusion criteria: * pregnant * inflammatory bowel disease * polyposis syndromes