Miracle-dz/UniFAR-FTUs huggingface dataset:
Measures for concordance and discordance with applications in disease control and prevention

Bivariate binary response data appear in many applications. Interest goes most often to a parameterization of the joint probabilities in terms of the marginal success probabilities in combination with a measure for association, most often being the odds ratio. Using, for example, the bivariate Dale model, these parameters can be modelled as function of covariates. But the odds ratio and other measures for association are not always measuring the (joint) characteristic of interest. Agreement, concordance, and synchrony are in general facets of the joint distribution distinct from association, and the odds ratio as in the bivariate Dale model can be replaced by such an alternative measure. Here, we focus on the so-called conditional synchrony measure. But, as indicated by several authors, such a switch of parameter might lead to a parameterization that does not always lead to a permissible joint bivariate distribution. In this contribution, we propose a new parameterization in which the marginal success probabilities are replaced by other conditional probabilities as well. The new parameters, one homogeneity parameter and two synchrony/discordance parameters, guarantee that the joint distribution is always permissible. Moreover, having a very natural interpretation, they are of interest on their own. The applicability and interpretation of the new parameterization is shown for three interesting settings: quantifying HIV serodiscordance among couples in Mozambique, concordance in the infection status of two related viruses, and the diagnostic performance of an index test in the field of major depression disorders.
Avaliação de métodos para superação de dormência de sementes de leguminosas arbóreas utilizadas na recuperação de áreas degradadas.

7 Introdução . 8 Material e Métodos . 11 Resultados e Discussão . 14 Cassia grandis cássia grande . 14 Mimosa artemisiana roseira . 17 Samanea tubulosa saman . 20 Enterolobium contortisiliquum orelha-de-negro . 22 Conclusão . 25 Referências Bibliográficas . 27 Avaliação de métodos para superação de dormência de sementes de leguminosas arbóreas utilizadas na recuperação de áreas degradadas André Luís Fonseca dos Santos1 Juliana Müller Freire2 Fatima C. M. Piña-Rodrigues3 1 Flora Tecnologia e Consultoria Ambiental Ltda. Rua Lincoln Correa, n. 89 Angra dos Reis/RJ. CEP 23900-000. E-mail: santosalf@hotmail.com 2 Pesquisadora. Embrapa Agrobiologia. Rodovia BR 465, km 7 Seropédica/RJ. CEP 23.890-000. E-mail: julianafreire@cnpab.embrapa. br 3 Professora da Universidade Federal de São Carlos Campus Sorocaba. Rodovia João Leme dos Santos, km 110 Sorocaba/SP. CEP 18.052-780. E-mail: fpina@ufscar.br Resumo O trabalho teve como objetivo estudar os métodos de superação de dormência tegumentar das espécies arbóreas Enterolobium contortisiliquum, Cassia grandis, Mimosa artemisiana e Samanea tubulosa. Foram avaliados os seguintes tratamentos, variando de acordo com cada espécie: 1. Testemunha (sementes intactas); 2. escarificação química com ácido sulfúrico (H2SO4) por 5, 10, 15, 20 e 30 minutos; 3. escarificação mecânica com lixa; 4. choque térmico seguido de imersão em água por 5, 10, 15 e 30 minutos, e também por 24 horas; 5. "joga e tira" em água quente com temperatura de aproximadamente 98oC. Após o tratamento, as sementes foram semeadas em areia, em caixas gerbox, e incubadas em germinador a 30oC. A porcentagem de germinação e o índice de velocidade de germinação (IVG) foram calculados. Houve diferença significativa (p < 0,05) para todos os tratamentos. Para Cassia grandis a imersão em ácido sulfúrico, independente do tempo utilizado, apresentou os melhores resultados de germinação e IVG, em relação à testemunha. Para Mimosa artemisiana, a imersão das sementes em água quente por 15 ou 30 minutos promoveu os maiores valores de germinação e IVG. A escarificação mecânica foi mais eficiente para as sementes de Samanea tubulosa. Para Enterolobium contortisiliquum recomenda-se a imersão das sementes em água quente, seguida de banho frio por cinco minutos.
TRIM59 overexpression correlates with poor prognosis and contributes to breast cancer progression through AKT signaling pathway

TRIM59 has been recently implicated in the carcinogenesis of several cancers such as lung cancer, gastric cancer, and bladder cancer. However, its expression pattern and clinical significance has not been investigated in human breast cancer. In the present study, we examined TRIM59 protein expression in 95 cases of breast cancer tissues using immunohistochemistry. We found that TRIM59 was upregulated in 42 out of 95 cases and correlated with TNM stage (P = 0.0056), lymph node metastasis (P = 0.0088) and poor prognosis (P = 0.0092). Importantly, TRIM59 level was higher in triple‐negative breast cancer (TNBC) (P = 0.0157). Expression of TRIM59 protein was also upregulated in breast cancer cell lines compared to normal MCF‐10A cell line. TRIM59 plasmid and shRNA transfection was performed in MCF‐7 and SK‐BR‐3 cells respectively. TRIM59 overexpression promoted cell proliferation, invasion, migration, cell cycle transition, and paclitaxel resistance, whereas TRIM59 depletion showed the opposite results. Further analysis showed that TRIM59 overexpression upregulated expression of cyclinA, cyclinE, Bcl‐xl, Bcl‐2, p‐AKT, and downregulated expression of p21, p27, p53. AKT inhibitor treatment abolished the effect of TRIM59 on Bcl‐2 expression. TRIM59 overexpression also upregulated the level of p53 ubiquitination. In conclusion, TRIM59 overexpression correlates with poor prognosis and promotes malignant behavior through regulation of AKT pathway in human breast cancer.
Comparative Effectiveness and Safety Between Milrinone or Dobutamine as Initial Inotrope Therapy in Cardiogenic Shock

Inotropes are an integral component of the early stabilization of the patient presenting with cardiogenic shock. Despite years of clinical experience with the 2 most commonly used inotropes, dobutamine and milrinone, there remains limited data comparing outcomes between the two. We conducted a retrospective review to compare the effectiveness and safety of milrinone or dobutamine for the initial management of cardiogenic shock. Adult patients with cardiogenic shock regardless of etiology who received initial inotrope therapy with either milrinone (n = 50) or dobutamine (n = 50) and did not receive mechanical circulatory support were included. The primary end point was the time to resolution of cardiogenic shock. Changes in hemodynamic parameters from baseline and adverse events were also assessed. Resolution of shock was achieved in similar numbers in both the groups (milrinone 76% vs dobutamine 70%, P = .50). The median time to resolution of shock was 24 hours in both groups (P = .75). There were no differences in hemodynamic changes during inotrope therapy, although dobutamine trended toward a greater increase in cardiac index. Arrhythmias were more common in patients treated with dobutamine than milrinone, respectively (62.9% vs 32.8%, P < .01), whereas hypotension occurred to a similar extent in both groups (milrinone 49.2% vs dobutamine 40.3%, P = .32). The use of concomitant vasoactive medications, dosage required, and duration of therapy did not differ between groups. There was no difference in the overall rate of discontinuation due to adverse event; however, milrinone was more commonly discontinued due to hypotension (13.1% vs 0%, P < .01) and dobutamine was more commonly discontinued due to arrhythmia (0% vs 11.3%, P < .01). Milrinone and dobutamine demonstrated similar effectiveness and safety profiles but with differences in adverse events. The choice of milrinone or dobutamine as initial inotrope therapy for cardiogenic shock may depend more on tolerability of adverse events.
Hydrogen sulfide improves postischemic neoangiogenesis in the hind limb of cystathionine‐β‐synthase mutant mice via PPAR‐γ/VEGF axis

Neoangiogenesis is a fundamental process which helps to meet energy requirements, tissue growth, and wound healing. Although previous studies showed that Peroxisome proliferator‐activated receptor (PPAR‐γ) regulates neoangiogenesis via upregulation of vascular endothelial growth factor (VEGF), and both VEGF and PPAR‐γ expressions were inhibited during hyperhomocysteinemic (HHcy), whether these two processes could trigger pathological effects in skeletal muscle via compromising neoangiogenesis has not been studied yet. Unfortunately, there are no treatment options available to date for ameliorating HHcy‐mediated neoangiogenic defects. Hydrogen sulfide (H2S) is a novel gasotransmitter that can induce PPAR‐γ levels. However, patients with cystathionine‐β‐synthase (CBS) mutation(s) cannot produce a sufficient amount of H2S. We hypothesized that exogenous supplementation of H2S might improve HHcy‐mediated poor neoangiogenesis via the PPAR‐γ/VEGF axis. To examine this, we created a hind limb femoral artery ligation (FAL) in CBS+/− mouse model and treated them with GYY4137 (a long‐acting H2S donor compound) for 21 days. To evaluate neoangiogenesis, we used barium sulfate angiography and laser Doppler blood flow measurements in the ischemic hind limbs of experimental mice post‐FAL to assess blood flow. Proteins and mRNAs levels were studied by Western blots and qPCR analyses. HIF1‐α, VEGF, PPAR‐γ and p‐eNOS expressions were attenuated in skeletal muscle of CBS+/− mice after 21 days of FAL in comparison to wild‐type (WT) mice, that were improved via GYY4137 treatment. We also found that the collateral vessel density and blood flow were significantly reduced in post‐FAL CBS+/− mice compared to WT mice and these effects were ameliorated by GYY4137. Moreover, we found that plasma nitrite levels were decreased in post‐FAL CBS+/− mice compared to WT mice, which were mitigated by GYY4137 supplementation. These results suggest that HHcy can inhibit neoangiogenesis via antagonizing the angiogenic signal pathways encompassing PPAR‐γ/VEGF axis and that GYY4137 could serve as a potential therapeutic to alleviate the harmful metabolic effects of HHcy conditions.
Therapeutic drug monitoring of tacrolimus and mycophenolic acid in outpatient renal transplant recipients using a volumetric dried blood spot sampling device

Tacrolimus and mycophenolic acid dosing after renal transplantation is individualized through therapeutic drug monitoring (TDM). Home‐based dried blood spot (DBS) sampling has the potential to replace conventional TDM sampling at the clinic. A liquid chromatography–tandem mass spectrometry (LC–MS/MS) assay was developed to quantify tacrolimus and mycophenolic acid in DBS and clinically validated for abbreviated area under the concentration–time curve (AUC) monitoring using an innovative volumetric DBS sampling device.
Impact of Knee Scooter Flexion Position on Venous Flow Rate

Background: The knee scooter is a commonly used mobility device in the setting of unilateral below-knee immobilization. The bent-knee posture has been shown to decrease venous flow in a seated position, but the knee scooter differs as the patient is weightbearing through the affected extremity. Our goal was to investigate the effects of knee scooter positioning on popliteal venous flow. Methods: Duplex ultrasonography was performed to obtain venous diameter and flow velocity of the popliteal vein on healthy subjects over the age of 18 without immobilization. Measurements were performed on the left knee of each subject while standing and with the same knee flexed on the knee scooter, by 2 physicians trained in ultrasound techniques. Mean velocity, peak velocity, vessel diameter, and volumetric flow rate were calculated and t tests were performed for each variable. A power analysis was performed, determining that 9 subjects would provide 80% power with an alpha of 0.05. A total of 13 subjects participated in the study. Mean age was 33 (range 20-56) years, with 6 females and 7 males. Results: Measurements of subjects while standing and on the knee scooter demonstrated a significant decrease in mean velocity (6.5 vs 3.2 cm/s, P < .01) and volumetric flow rate (227.8 vs 106.2 mL/min, P < .01) while subjects were using the scooter. Vessel diameter (0.82 vs 0.78 cm, P = .15) and peak velocities (19.8 vs 14.7 cm/s, P = .19) were not significantly different between standing and kneeling positions. Conclusion: Our findings demonstrated a statistically significant decrease in volumetric flow rate in subjects using a knee scooter device with a flexed knee. Although venous stasis is a known risk factor for DVT, flow rate thresholds for increased thrombus formation are not well defined. The duration of scooter use, or flexed knee positioning, may have some effect on the degree of stasis. This finding should caution orthopedists to consider the risk attributed to the knee scooter as part of their overall patient assessment. Level of Evidence: Level II, therapeutic, comparative study.
Retrieve-and-Read: Multi-task Learning of Information Retrieval and Reading Comprehension

This study considers the task of machine reading at scale (MRS) wherein, given a question, a system first performs the information retrieval (IR) task of finding relevant passages in a knowledge source and then carries out the reading comprehension (RC) task of extracting an answer span from the passages. Previous MRS studies, in which the IR component was trained without considering answer spans, struggled to accurately find a small number of relevant passages from a large set of passages. In this paper, we propose a simple and effective approach that incorporates the IR and RC tasks by using supervised multi-task learning in order that the IR component can be trained by considering answer spans. Experimental results on the standard benchmark, answering SQuAD questions using the full Wikipedia as the knowledge source, showed that our model achieved state-of-the-art performance. Moreover, we thoroughly evaluated the individual contributions of our model components with our new Japanese dataset and SQuAD. The results showed significant improvements in the IR task and provided a new perspective on IR for RC: it is effective to teach which part of the passage answers the question rather than to give only a relevance score to the whole passage.
Latent Space Temporal Model of Microbial Abundance to Predict Domination and Bacteremia.

Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal microbiomes that takes into account interaction among bacteria as well as external effects such as antibiotics. The model successfully deals with pragmatic issues such as random measurement error and varying time intervals between measurements through latent space modeling. We demonstrate utility of the model by using latent state features to predict the clinical events of intestinal domination and bacteremia, improving accuracy over existing methods. We further leverage this framework to validate known links between antibiotics and clinical outcomes, while discovering new ones.
Midterm Results after Open versus Arthroscopic Transosseous Repair for Foveal Tears of the Triangular Fibrocartilage Complex

Abstract Purpose Various surgical procedures for foveal tears of the triangular fibrocartilage complex (TFCC) have been reported, and the procedures can be grossly divided into open and arthroscopic repair. The surgical results of both procedures were compared. Materials and Methods Twenty-nine patients underwent repair of a TFCC foveal tear. The 13 men and 16 women were in the age range of 14 to 72 years (average age, 30 years). Five patients had a history of distal radius fractures that healed uneventfully with nonoperative treatment. The mean duration of symptoms before surgery was 7.1 months. The procedure for repair consisted of 8 open repairs and 21 arthroscopic repairs. In both procedures, the TFCC was repaired transosseously to the ulna. The mean follow-up period was 34.4 (range, 24–70) months. The patients' pain, range of motion (ROM), grasping power, ulnar head instability, Disabilities of the Arm, Shoulder and Hand questionnaire (DASH), and Mayo modified wrist score (MMWS) were evaluated. The operating time was also compared. Results There were no significant differences between the groups in pain, ROM, grasping power, ulnar head instability, and DASH. The MMWS was excellent in 8 patients in the open repair group, with 18 excellent and 3 good in the arthroscopic repair group. The mean operating time was significantly shorter for arthroscopic repair than for open repair. Conclusion Satisfactory outcomes were achieved for both open and arthroscopic repair techniques in the midterm. If a surgeon becomes familiar with the arthroscopic repair, the arthroscopic technique would be more feasible than the open repair in terms of technical facility and shortening of the operating time. Level of Evidence Level III, therapeutic study.
Primitive Magmas in the Early Central American Volcanic Arc System Generated by Plume-Induced Subduction Initiation

Primitive lavas with Mg# ≥60 have been identified in the literature from the Sona-Azuero, Golfito and Chagres-Bayano forearc segments of southern Costa Rica and Panama of the early (75-39 Ma) Central American Volcanic Arc system (CAVAS). Primitive CAVAS basalts are remarkably similar in terms of major and many trace elements to primitive MORB and primitive basalts of the Mariana Arc. Significant differences however, are apparent between primitive lavas of Chagres-Bayano relative to those of Sona-Azuero and Golfito. Primitive Chagres-Bayano lavas record much higher degrees of partial melting and higher amounts of shallow and deep subduction additions (e.g., higher Ba/Th, Th/Nb) than those of the older Sona-Azuero and Golfito arc segments which reflects the early petrologic and tectonic evolution of the CAVAS which is similar to other forearc systems. As shown in previous studies, early CAVAS lavas are exceptionally similar in radiogenic isotopic composition to those of the Caribbean Large Igneous Province (CLIP) oceanic plateau at 90 Ma, the approximate timing of onset of the volumetrically dominant phase of CLIP magmatism. This recognition is consistent with subduction initiation models which require plume-subduction interaction. Such models also dictate that an elevated sub-arc thermal anomaly was present at inception of the CAVAS. It is postulated that in addition to providing an anomalously high temperature regime in the sub-arc mantle at inception of the CAVAS, that extrusion of the CLIP also resulted in lithospheric weakening and extension which allowed for production and rapid ascent of a high percentage of primitive lavas.
Gender and Mortality after Radical Cystectomy: Competing Risk Analysis

Background: Data on the impact of gender on mortality after radical cystectomy is conflicting. We investigated a large single center sample with long-term follow-up in order to determine the relationship between gender and outcome. Patients and Methods: A total of 1,184 consecutive patients who underwent radical cystectomy for high risk superficial or muscle-invasive urothelial or undifferentiated bladder cancer between 1993 and 2015 were stratified by gender. Demographic data was compared using Mann-Whitney U test, chi-square test, or Fisher exact test. Cox proportional hazard models were used for the analysis of competing risks and logit models were used for the prediction of the receipt of adjuvant cisplatin-based chemotherapy. Results: Female patients were older, healthier, less frequently current smokers and had more extravesical tumors. In the multivariate analyses, female gender was an independent predictor of (lower) non-bladder cancer (competing) mortality (hazards ratio [HR] 0.68, 95% CI 0.49–0.95, p = 0.0248) but no predictor of bladder cancer-specific mortality (HR in the full model 1.20, 95% CI 0.94–1.54, p = 0.15). Gender was no predictor of the receipt of adjuvant cisplatin-based chemotherapy. Conclusions: Female gender was associated with an increased risk of extravesical disease but was no independent predictor of bladder cancer-specific mortality. Anatomical differences might be a plausible explanation for these observations.
Clinical Applications of Neuroimaging in Psychiatric Disorders.

In response to claims being made that brain imaging technology had already reached the point at which it could be useful for making a clinical diagnosis and for helping in treatment selection in individual patients, the APA Assembly passed an action paper calling for the development of an APA Position Paper on the Clinical Application of Brain Imaging in Psychiatry. Consequently, a workgroup was appointed under the auspices of the APA Council on Research to develop an evidenced-based review of the current state of the art of the clinical utility of brain imaging for psychiatric diagnosis and for predicting treatment response. The review focused on the following diagnostic areas: adult mood and anxiety disorders, psychotic disorders, cognitive disorders, substance use disorders, and childhood disorders, including attention deficit hyperactivity disorder, childhood bipolar disorder, depression/anxiety, and autism spectrum disorder. This review was approved by the APA Board of Trustees as a resource document. The review is summarized below, and the full resource document is available in a data supplement accompanying the online version of this APA Official Action (ajp.psychiatryonline.org).
Prehypertension during pregnancy and risk of small for gestational age: a systematic review and meta-analysis

Abstract Objective: Emerging evidence shows that high blood pressure (BP) level even below 140/90 mmHg during pregnancy is associated with increased risk for maternal and infant complications. The meta-analysis evaluated the associations between prehypertension (BP 120–139/80–89 mmHg) during pregnancy and the risk of small for gestational age (SGA), as well as the impact of prehypertension on birth weight (BW). Methods: Databases (PubMed, Embase, and Cochrane Library) were searched for cohort studies with data on prehypertension in pregnancy and adverse obstetrical outcomes, including SGA and/or BW. The relative risks (RRs) of SGA and weighted mean differences (WMD) in BW were calculated and reported with 95% confidence intervals (95% CIs). We calculated pooled RRs using fixed- and random-effects models. Results: A total of 143,835 participants from five cohort studies were included. Prehypertension in pregnancy increased the risk of SGA (RR 1.59, 95%CI 1.44 to 1.76, p < .00001) and lowered BW (WMD −13.71, 95% CI −83.28 to 55.87, p = .70) compared with optimal BP (<120/80 mmHg). In subgroup analyses, for prehypertension in late pregnancy, the risk of SGA was significantly higher than for optimal BP (RR 1.60, 95% CI 1.44 to 1.78). Conclusion: BP within the range of 120–139/80–89 mmHg during pregnancy, as previously defined as prehypertension, particularly in late pregnancy, was associated with a 59% increase in the risk of having an SGA birth.
Consistent Least Squares Estimator for Co-Array-Based DOA Estimation

Sparse linear arrays (SLAs), such as nested and co-prime arrays, have the attractive capability of providing enhanced degrees of freedom by exploiting the co-array model. Accordingly, co-array-based Direction of Arrivals (Doas) estimation has recently gained considerable interest in array processing. The literature has suggested applying MUSIC on an augmented sample covariance matrix for co-array-based Doas estimation. In this paper, we propose a Least Squares (LS) estimator for co-array-based DoAs estimation employing the covariance fitting method as an alternative to MUSIC. We show that the proposed LS estimator provides consistent estimates of Doas of identifiable sources for SLAs. Additionally, an analytical expression for the large sample performance of the proposed estimator is derived. Numerical results illustrate the finite sample behavior in relation to the derived analytical expression. Moreover, the performance of the proposed LS estimator is compared to the co-array-based MUSIC.