Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-Rank Tucker-2 Model for Multi-Subject fMRI Data Decomposition With Spatial Sparsity Constraint

Tucker decomposition can provide an intuitive summary to understand brain function by decomposing multi-subject fMRI data into a core tensor and multiple factor matrices, and was mostly used to extract functional connectivity patterns across time/subjects using orthogonality constraints. However, these algorithms are unsuitable for extracting common spatial and temporal patterns across subjects due to distinct characteristics such as high-level noise. Motivated by a successful application of Tucker decomposition to image denoising and the intrinsic sparsity of spatial activations in fMRI, we propose a low-rank Tucker-2 model with spatial sparsity constraint to analyze multi-subject fMRI data. More precisely, we propose to impose a sparsity constraint on spatial maps by using an $ \ell _{p} $ norm ( ${0}< {p}\le {1}$ ), in addition to adding low-rank constraints on factor matrices via the Frobenius norm. We solve the constrained Tucker-2 model using alternating direction method of multipliers, and propose to update both sparsity and low-rank constrained spatial maps using half quadratic splitting. Moreover, we extract new spatial and temporal features in addition to subject-specific intensities from the core tensor, and use these features to classify multiple subjects. The results from both simulated and experimental fMRI data verify the improvement of the proposed method, compared with four related algorithms including robust Kronecker component analysis, Tucker decomposition with orthogonality constraints, canonical polyadic decomposition, and block term decomposition in extracting common spatial and temporal components across subjects. The spatial and temporal features extracted from the core tensor show promise for characterizing subjects within the same group of patients or healthy controls as well.
Somatic mosaicism detected by genome-wide sequencing in 500 parent–child trios with suspected genetic disease: clinical and genetic counseling implications

Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
Population Pharmacokinetics of Ponatinib in Healthy Adult Volunteers and Patients With Hematologic Malignancies and Model‐Informed Dose Selection for Pediatric Development

The BCR‐ABL1 inhibitor ponatinib is approved for the treatment of adults with chronic myeloid leukemia or Philadelphia chromosome–positive acute lymphoblastic leukemia, including those with the T315I mutation. We report a population pharmacokinetic model‐based analysis for ponatinib and its application to inform dose selection for pediatric development. Plasma concentration–time data were collected from 260 participants (86 healthy volunteers; 174 patients with hematologic malignancies) enrolled across 7 clinical trials. Data were analyzed using nonlinear mixed‐effects modeling. Ponatinib pharmacokinetics were described by a 2‐compartment model with first‐order elimination from the central compartment. The final model included body weight and age as covariates on the apparent central volume of distribution; however, exposure variability explained by these covariates was small compared with overall variability in the population. None of the covariates evaluated, including sex, age (19‐85 years), race, body weight (40.7‐152.0 kg), total bilirubin (0.1‐3.16 mg/dL), alanine aminotransferase (6‐188 U/L), albumin (23.0‐52.5 g/L), and creatinine clearance (≥28 mL/min) had clinically meaningful effects on apparent oral clearance. Simulations based on the final model predicted that daily doses of 15 to 45 mg result in steady‐state average concentrations that are in the pharmacological range for BCR‐ABL1 inhibition and approximate or exceed concentrations associated with suppression of T315I mutant clones. The final model was adapted using allometric scaling to inform dose selection for pediatric development. Clinicaltrials.gov identifier: NCT00660920; NCT01667133; NCT01650805
Use of a vaginal CO2 laser for the management of genitourinary syndrome of menopause in gynecological cancer survivors: a systematic review

Abstract Genitourinary syndrome of menopause (GSM) may arise from the hypoestrogenism caused by ovarian function destruction following gynecological cancer treatments. GSM may also be present in menopausal women and its symptoms might be exacerbated by cancer treatments. Historically, patients with hormone-dependent gynecological cancer and physicians have been less comfortable using vaginal estrogen due to fear of recurrence. CO2 vaginal laser therapies have demonstrated efficacy as a non-hormonal alternative for GSM treatment in healthy menopausal patients. The objective of this study was to evaluate the data on the effect of a CO2 vaginal laser for the management of GSM in gynecological cancer patients. Databases searched included MEDLINE, Embase, PubMed, Cochrane and Google Scholar. Selected studies assessed use of a CO2 vaginal laser in gynecological cancer patients with GSM. A total of 269 studies were retrieved. Four studies met the inclusion criteria. Each study followed a different type of CO2 vaginal laser protocol for the management of GSM in gynecological cancer patients. There are no randomized controlled trials that assess the use of a CO2 vaginal laser in gynecologic cancer patients. The number of published gynecological cancer patients treated with a CO2 laser for the management of GSM is extremely limited (N < 100). There is a lack of literature on the impact and safety of vaginal CO2 laser use to manage GSM in gynecologic cancer patients.
Antimicrobial and cytotoxic activity to human colon adenocarcinoma cell lines (HT-29) potential of olive oil extraction residue

Abstract In the Olive drupe (Olea europaea L.) oil extraction process, 80% of the volume generated is waste (bagasse). Advancing the expansion of the olive oil market, it is necessary to develop alternatives that, in addition to adding value to industrial waste, also reduce possible environmental damage. Our study aimed to understand the antimicrobial and Cytotoxic activity potential of the residues from the extraction of olive oil from the blend of the varieties Arbequina and Arbosana. The extract shows cytotoxic activity, inhibiting about 75% of cancer cells in the human colon at a concentration of 0.15 mg of Gallic Acid equivalent (GAE)/mL. The effectiveness of the extract against microorganisms often associated with foodborne diseases and food decomposition has also been discovered, without compromising the microorganisms responsible for fermentation. Thus, this study provides future perspectives for the use of active ingredients extracted from the residue from the extraction of olive oil. Graphical Abstract
Responses of Sinus Membrane and Antral Pseudocyst Following Lateral Window Sinus Augmentation with Bone Grafting: A Retrospective Study.

PURPOSE To investigate the influence of lateral window sinus augmentation on sinus physiology, including sinus membrane thickness and the outcome of antral pseudocysts. MATERIALS AND METHODS This retrospective study was performed by reviewing all lateral window sinus augmentation procedures, which were done between the years 2013 and 2015. Each enrolled patient had CBCT images preoperatively (T0), immediately postoperatively (T1), and 6 months postoperatively (T2). The sinus membrane thickness, pseudocyst dimensions, and intraoperative perforation were evaluated. Patient-related factors such as age and sex that could influence the mucosal properties were also analyzed. RESULTS Based on established inclusion criteria, 306 patients with 320 sinuses were included in this study. The overall mean thickness of the sinus membrane (T0) was 1.30 ± 1.08 mm, and membrane thickening (> 2 mm) was observed in 22.19% of the sinuses. Preexisting pseudocysts were identified in 24 sinuses (7.50%), most of which remained unchanged or disappeared after 6 months. The intraoperative membrane perforation rate was lowest (1.96%) when the membrane thickness was 1.0 to 1.5 mm, and the perforation rate was increased in patients with thickened (> 2 mm) or thinned (≤ 1 mm) membrane. Membranes swelled immediately after operation (T1 vs T0, P < .01) and gradually recovered at 6 months. No significant change in membrane thickness was shown after the sinus augmentation procedure in the perforation group and pseudocyst group. The mean thickness of the sinus membrane at T0 and T1 was significantly higher for male subjects (P < .01). CONCLUSION Lateral window sinus augmentation has little or no impact on sinus membrane thickness and antral pseudocysts after a 6-month healing period, except for a transient mild membrane swelling. Thickened and thinned membrane were risk factors for intraoperative perforation. Small-sized perforation and pseudocysts might not contraindicate sinus augmentation from the standpoint of the surgical impact on the sinus membrane.
Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing

Research efforts to combat antimalarial drug resistance rely on quick, robust, and sensitive methods to genetically characterize Plasmodium falciparum parasites. We developed a single-nucleotide polymorphism (SNP)-based genotyping method that can assess 33 drug resistance-conferring SNPs in dhfr, dhps, pfmdr1, pfcrt, and k13 in nine PCRs, performed directly from P. falciparum cultures or infected blood. ABSTRACT Research efforts to combat antimalarial drug resistance rely on quick, robust, and sensitive methods to genetically characterize Plasmodium falciparum parasites. We developed a single-nucleotide polymorphism (SNP)-based genotyping method that can assess 33 drug resistance-conferring SNPs in dhfr, dhps, pfmdr1, pfcrt, and k13 in nine PCRs, performed directly from P. falciparum cultures or infected blood. We also optimized multiplexed fragment analysis and gel electrophoresis-based microsatellite typing methods using a set of five markers that can distinguish 12 laboratory strains of diverse geographical and temporal origin. We demonstrate how these methods can be applied to screen for the multidrug-resistant KEL1/PLA1/PfPailin (KelPP) lineage that has been sweeping across the Greater Mekong Subregion, verify parasite in vitro SNP-editing, identify novel recombinant genetic cross progeny, or cluster strains to infer their geographical origins. Results were compared with Illumina-based whole-genome sequence analysis that provides the most detailed sequence information but is cost-prohibitive. These adaptable, simple, and inexpensive methods can be easily implemented into routine genotyping of P. falciparum parasites in both laboratory and field settings.
Coronavirus Disease Contact Tracing Outcomes and Cost, Salt Lake County, Utah, USA, March–May 2020

Outcomes and costs of coronavirus disease (COVID-19) contact tracing are limited. During March–May 2020, we constructed transmission chains from 184 index cases and 1,499 contacts in Salt Lake County, Utah, USA, to assess outcomes and estimate staff time and salaries. We estimated 1,102 staff hours and $29,234 spent investigating index cases and contacts. Among contacts, 374 (25%) had COVID-19; secondary case detection rate was ≈31% among first-generation contacts, ≈16% among second- and third-generation contacts, and ≈12% among fourth-, fifth-, and sixth-generation contacts. At initial interview, 51% (187/370) of contacts were COVID-19–positive; 35% (98/277) became positive during 14-day quarantine. Median time from symptom onset to investigation was 7 days for index cases and 4 days for first-generation contacts. Contact tracing reduced the number of cases between contact generations and time between symptom onset and investigation but required substantial resources. Our findings can help jurisdictions allocate resources for contact tracing.
Comparing the Clinical Outcome of Peri-implant Hard and Soft Tissue Treated with Immediate Individualized CAD/CAM Healing Abutments and Conventional Healing Abutments for Single-Tooth Implants in Esthetic Areas Over 12 Months: A Randomized Clinical Trial.

PURPOSE The purpose of this study was to compare the clinical influence of immediate individualized CAD/CAM healing abutments and conventional healing abutments on peri-implant soft and hard tissue in shaping the emergence profile. MATERIALS AND METHODS Patients with a single maxillary incisor missing who accepted dental implantation were registered in this study. After implantation, individualized CAD/CAM healing abutments and regular prefabricated abutments were randomly inserted to shape the emergence profile. A radiograph was taken, and the pink esthetic score, papilla height, papilla proportion, and probing depth were recorded at 6 months after implant placement (T1), loading (T2, definitive restoration), and 1 year after loading (T3). Patient self-assessment scores were also evaluated through the visual analog scale. The data were analyzed statistically using the t test or repeated-measurements analysis of variance (ANOVA). RESULTS Twenty patients were enrolled in this study, including 9 patients using individualized abutments and 11 patients using conventional abutments. The mean total marginal bone level in the individualized abutment group was 1.53 ± 0.65 mm at implant placement, 1.10 ± 0.47 mm at loading, and 0.76 ± 0.47 mm at 1 year after loading. In contrast, the mean total marginal bone level in the conventional abutment group was 0.62 ± 0.39 mm at implant placement, 0.14 ± 0.55 mm at loading, and -0.04 ± 0.53 mm at 1 year after loading. The differences between the individualized abutment group and conventional abutment group were statistically significant for the mesial and distal marginal bone level at three time points, respectively (P ≤ .05). Similarly, there were significant differences in probing depth, papilla height, and pink esthetic score between the two groups. CONCLUSION This immediately individualized healing abutment protocol may significantly preserve the peri-implant marginal bone and soft tissue. The use of individualized CAD/CAM healing abutments for shaping the emergence profile shows better esthetic outcomes than conventional healing abutments.
Development and psychometric evaluation of a Thai Diagnostic Autism Scale for the early diagnosis of Autism Spectrum Disorder

The Thai Diagnostic Autism Scale (TDAS) was developed for use as a diagnostic tool for the early diagnosis of Autism Spectrum Disorder (ASD) in Thai children aged 12–48 months old. TDAS consists of 23 items (13 and 17 items in the observational and interview sections, respectively) classified into seven domains (A1–A3 and B1–B4) according to the criteria in the Diagnostic and Statistical Manual of Mental Disorder, fifth edition (DSM‐5). Children with a single score in the A1–A3 domains and at least two of the B1–B4 domains were classified with ASD. The item‐objective congruence (IOC) index, confirmatory factor analysis, and Kappa coefficient were used to evaluate the content, constructs, and inter‐rater validity levels between the evaluators and concurrent validity between TDAS and physicians' diagnoses, respectively. TDAS showed good overall content validity (IOC range 0.71–1.00), suitable construct validity (root‐mean‐squared errors of approximation of 0.076 and 0.067, comparative fit indexes of 0.902 and 0.858, and Tucker‐Lewis indexes of 0.882 and 0.837 for the observation and interview sections, respectively), and excellent diagnostic agreement between TDAS and the evaluators (Kappa = 1.000) as well as between TDAS and the physicians' diagnoses (Kappa = 0.871). The sensitivity and specificity of TDAS were 100% and 82.4%, respectively. In conclusion, TDAS yielded a high level of content validity, concurrent validity, and inter‐rater reliability for the early diagnosis of ASD in Thai children. A large‐scale study using TDAS is needed to determine an appropriate cut‐off point as well as its efficacy.
Evaluation of Usability of the Tiger Full Foot 3D Scanner for the Measurements of Basic Foot Dimensions in Clinical Practice.

BACKGROUND Foot dimension information is important both for footwear design and clinical applications. In recent years, non-contact three-dimensional foot digitizers/scanners became popular as they are non-invasive and are both valid and reliable for the most of measures. Some of them also offer automated calculations of basic foot dimensions. The study aimed to determine test-retest reliability, objectivity, and concurrent validity of the Tiger full foot 3D scanner as well as the relationship between the manual measures of the medial longitudinal arch of the foot and its alternative parameters obtained automatically by the scanner. METHODS Intraclass correlation coefficients and the values of minimal detectable change were used to assess the reliability and objectivity of the scanner. Concurrent validity and the relationship between the arch height measures were determined by the Pearson's correlation coefficient and the limits of agreement between the scanner and the calliper method. RESULTS Both the relative and absolute agreement between the repeated measurements obtained by the scanner show excellent reliability and objectivity of linear measures and only good to nearly good test-retest reliability and objectivity of the arch height. Correlations between the values obtained by the scanner and the calliper were generally higher in linear measures (rp{greater than or equal to}0.929). The representativeness of state of bony architecture by the soft tissue margin of the medial foot arch demonstrate the lowest correlations among the all measurements (rp{less than or equal to}0.526). CONCLUSIONS The Tiger full foot 3D scanner offers both excellent reliability and objectivity in linear measures, which correspond to those obtained by the calliper method. However, values obtained by the both methods shouldn't be used interchangeably. The arch height measure is less accurate, which could limit its use in some clinical applications. Orthotists and related professions probably appreciate scanner more than other specialists.
Amelioration of Diabetic Nephropathy by Targeting Autophagy via Rapamycin or Fasting: Relation to Cell Apoptosis/Survival

Autophagy has been demonstrated to have a beneficial effect on diabetic nephropathy (DN). Rapamycin, an inhibitor of mTOR, was shown to stimulate β-cell autophagy. However, its effects on preventing or ameliorating DN is unclear, and its effects are worth studying. As fasting is now an attractive protective strategy, we aim to compare its effect to rapamycin effects on pancreatic and renal cells. Twenty-eight adult male Wistar Albino rats were randomly divided into four groups, using streptozotocin (STZ) to induce diabetes mellitus (DM). Autophagy was induced by two ways; rapamycin or fasting. The extent of autophagy and apoptosis were investigated by measuring the level of LC3B and p53 proteins, respectively, in pancreatic and kidney tissues using Western blotting (WB) technique and imaging the renal cells under transmission electron microscope. The efflux transporter P-glycoprotein was quantified by WB as well. Rapamycin-induced autophagy occurred concurrently with apoptosis. On the other hand, fasting supported P-glycoprotein recovery and renal cell survival together with disabling β-cells apoptosis. In conclusion, this study provides a potential link between rapamycin or fasting for the cross-regulation of apoptosis and autophagy in the setting of cell stress as DN. Unlike rapamycin, fasting enhanced the active expression of ABCB1 efflux protein, providing insights on the potential ameliorative effects of fasting in DN that require further elucidation.
The Effect of Zbxz23ir-21 NANO(nanomaterials) Delivery Vector on Apoptosis and PTEN(phosphatase and tensin homolog deleted on chromosome ten)/PI3K(Intracellular phosphatidylinositol kinase)/AKT(related to the A and C kinase) in Children with CHOLESTEATOMA in Middle Ear

ABSTRACT Cholesteatoma of the middle ear is a kind of cystic disease with clear boundary formed by the abnormal growth of keratosquamous epithelium in temporal bone. Cholesteatoma otitis caused by it is a common disease in otorhinolaryngology. The EPR effect promotes the selective distribution of macromolecular substances in tumor tissues, which can increase drug efficacy. The purpose of this paper is to prepare and deliver the mir34a small molecule regulator, rubine, by nanotechnology, and to deliver it to the cells successfully. It can passively target tumor tissue through EPR effect, and play its regulatory role on miR-34a, thus inhibiting the growth of cholesteatoma cells. The effects of nano delivery on apoptosis and PIEN/P13K/AKt of children with middle ear choledochoma were tested in this paper. The experimental results were conducted on cholesteatoma cells as cell lines and balb/c nude mice as experimental objects. The expression of PTEN/PI3K/AKT in experimental group and control group was detected by immunohistochemistry. Apoptosis was discussed by cell activity detection. The physical and chemical properties, encapsulation efficiency, drug release ability in vitro and antitumor activity of nanoparticles in vitro and in vivo were studied. The results of cell level experiments in vitro showed that free RUBINE caused about 15% apoptosis, which was not different from RC NPs. The results showed that the nanoparticles could improve the expression of miR-34 in the cells, and then regulate the expression of Bcl-2, Cdk6 and CyclinD1, and play the inhibitory effect of miR-34a on the proliferation and migration of tumor cells.