Miracle-dz/UniFAR-FTUs huggingface dataset:
A preliminary study of the potential of tree classifiers in triage of high-grade squamous intraepithelial lesions.

OBJECTIVE To investigate the potential value of tree classifiers for the triage of high-grade squamous intraepithelial lesions. STUDY DESIGN The dataset comprised 808 histologically confirmed cases having a complete range of the cytologic sample assessments--liquid-based cytology, reflex human papillomavirus (HPV) DNA test, E6/E7 HPV mRNA test, and p16 immunocytochemical examinations. Data include 488 histologically negative (cervical intraepithelial neoplasia [CIN] 1 and below) or clinically negative cases and 320 with histologic diagnosis of CIN 2 or worse. Cytologic diagnosis was made according to the criteria of the Bethesda System. Cases were classified in two groups according to histology: those with CIN 2 or worse and those with CIN 1 and below. Fifty percent were randomly selected as a training set and the remaining were as a test set. RESULTS Application of tree classifier on the test set gave correct classification of 66.9% for CIN 2 and above cases and 97.3% for CIN 1 and below, producing overall accuracy of 91.5%, outperforming cytologic diagnosis alone. CONCLUSION Application of tree classifiers, based on standard cytologic diagnosis and expression of studied biomarkers, produces improved classification results for cervical precancerous lesions and cancer diagnosis and
Impact of Conversion From Advagraf to Twice-Daily Generic Tacrolimus in Kidney Transplant Recipients: A Single-Center Study—A 3-Year Follow-Up

Tacrolimus is a key immunosuppression drug in solid organ transplantation with a narrow therapeutic index. Twice-daily brand tacrolimus Prograf to once-daily brand tacrolimus Advagraf conversion was proven to be safe as was Prograf to twice-daily generic tacrolimus (Sandoz). Our group previously published the first study comparing the clinical outcomes of renal transplant patients switched from Advagraf to generic tacrolimus with good results at 9-month follow-up. We sought to find if the conversion was still considered safe at 36 months. We included patients with stable renal function, serum creatinine less than 2.0mg/dL, transplanted for 6months or longer. Tacrolimus conversion was performed on a 1 mg:1 mg basis. Thereafter, doses were adjusted to maintain target trough levels between 5 and 10 ng/mL. Our main endpoints were patient and graft survival at 12, 24, and 36months. Secondary endpoints included evolution of serum creatinine
Efficacy of stereotactic body radiotherapy for hepatocellular carcinoma with portal vein tumor thrombosis/inferior vena cava tumor thrombosis: evaluation by comparison with conventional three-dimensional conformal radiotherapy

This study aimed to evaluate the efficacy of stereotactic body radiotherapy (SBRT) compared with three-dimensional conformal radiotherapy (3DCRT). Forty-three patients with portal vein tumor thrombosis (PVTT)/inferior vena cava tumor thrombosis (IVCTT) treated with SBRT (27 with CyberKnife (CK) and 16 with TrueBeam (TB)) from April 2013 to December 2014, and 54 treated with 3DCRT from June 2008 to March 2013 were evaluated. Dosimetric parameters, response to radiotherapy (RT) and survival outcomes were compared in total SBRT vs. 3DCRT, CK vs. 3DCRT and TB vs. 3DCRT, respectively. The median biologically effective dose 10 (BED10) values in total SBRT, CK, TB and 3DCRT were 73.4 Gy10, 75.0 Gy10, 60.5 Gy10 and 58.5 Gy10, respectively (P < 0.001 in total SBRT vs. 3DCRT, P < 0.001 in CK vs. 3DCRT, P = 0.004 in TB vs. 3DCRT). The tumor response rates were 67%, 70%, 62% and 46%, respectively (P = 0.04, P = 0.04, P = 0.25). The 1-year overall survival rates were 49.3%, 56.7%, 38.1% and 29.3%, respectively (P = 0.02, P = 0.02, P = 0.30), and the 1-year local progression rates were 20.4%, 21.9%, 18.8% and 43.6%, respectively (P = 0.01, P = 0.04, P = 0.10). The use of SBRT made it possible to achieve a higher BED10 compared with the use of 3DCRT. Improvements in local control and survival were achieved in the CK group and the total SBRT group. Our results suggest that SBRT may have the potential to be the standard RT technique for the treatment of PVTT/IVCTT.
Radiomic analysis reveals DCE-MRI features for prediction of molecular subtypes of breast cancer

The purpose of this study was to investigate the role of features derived from breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and to incorporated clinical information to predict the molecular subtypes of breast cancer. In particular, 60 breast cancers with the following four molecular subtypes were analyzed: luminal A, luminal B, human epidermal growth factor receptor-2 (HER2)-over-expressing and basal-like. The breast region was segmented and the suspicious tumor was depicted on sequentially scanned MR images from each case. In total, 90 features were obtained, including 88 imaging features related to morphology and texture as well as dynamic features from tumor and background parenchymal enhancement (BPE) and 2 clinical information-based parameters, namely, age and menopausal status. An evolutionary algorithm was used to select an optimal subset of features for classification. Using these features, we trained a multi-class logistic regression classifier that calculated the area under the receiver operating characteristic curve (AUC). The results of a prediction model using 24 selected features showed high overall classification performance, with an AUC value of 0.869. The predictive model discriminated among the luminal A, luminal B, HER2 and basal-like subtypes, with AUC values of 0.867, 0.786, 0.888 and 0.923, respectively. An additional independent dataset with 36 patients was utilized to validate the results. A similar classification analysis of the validation dataset showed an AUC of 0.872 using 15 image features, 10 of which were identical to those from the first cohort. We identified clinical information and 3D imaging features from DCE-MRI as candidate biomarkers for discriminating among four molecular subtypes of breast cancer.
Asperger syndrome in males over two decades: stability and predictors of diagnosis.

OBJECTIVE To examine the diagnostic stability of a childhood diagnosis of Asperger Syndrome (AS) into adulthood in a prospective longitudinal study, and identify the predictors of stability. METHODS One hundred males with AS diagnosed in childhood (T0) according to Gillberg's AS criteria, were followed up prospectively into adulthood over an average of 19 years (range 13-26 years). Fifty males (mean age 30 years) participated in this second follow-up (T2) of the cohort. Seventy-six had participated in a previous follow-up (T1) at mean age 22 years (47 participated in both follow-ups). Diagnosis at T2 was assessed using three sets of diagnostic criteria (Gillberg's AS criteria, DSM-IV Pervasive Developmental Disorder (PDD) and DSM-5 Autism Spectrum Disorder (ASD) criteria) and compared to previous assessments. Background predictors of diagnostic stability were analyzed. General functioning at T2 was assessed and compared to T1. RESULTS There was a decline in the stability of AS diagnosis over time, the rate dropping from 82% at T1 to 44% at T2, when using the Gillberg criteria. There was also a significant decrease in the rate of cases fulfilling any PDD diagnosis according to the DSM-IV, from 91% at T1 to 76% at T2 in the 47 cases followed up twice. Severity of autism spectrum symptoms at T1 was the main predictor of diagnostic stability at T2. Twenty percent of those meeting criteria for a PDD diagnosis according to DSM-IV, did not meet DSM-5 ASD criteria although they had marked difficulties in everyday life. CONCLUSION Asperger Syndrome, when considered as an ASD/PDD diagnosis, was fairly stable into adulthood, but there was a significant increase over time in cases no longer meeting criteria for an ASD diagnosis according to the DSM-IV, or AS according to the Gillberg criteria. Cases with a stable diagnosis showed significantly more core ASD symptoms in adolescence/young adulthood.
Sexual transmission of the [Het-s] prion leads to meiotic drive in Podospora anserina

In the filamentous fungus Podospora anserina, two phenomena are associated with polymorphism at the het-s locus, vegetative incompatibility and ascospore abortion. Two het-s alleles occur naturally, het-s and het-S. The het-s encoded protein is a prion propagating as a self-perpetuating amyloid aggregate. When prion-infected [Het-s] hyphae fuse with [Het-S] hyphae, the resulting heterokaryotic cells necrotize. [Het-s] and [Het-S] strains are sexually compatible. When, however, a female [Het-s] crosses with [Het-S], a significant percentage of het-S spores abort, in a way similar to spore killing in Neurospora and Podospora. We report here that sexual transmission of the [Het-s] prion after nonisogamous mating in the reproductive cycle of Podospora is responsible for the killing of het-S spores. Progeny of crosses between isogenic strains with distinct wild-type or introduced, ectopic het-s/S alleles were cytologically and genetically analyzed. The effect of het-s/S overexpression, ectopic het-s/S expression, absence of het-s expression, loss of [Het-s] prion infection, and the distribution patterns of HET-s/S-GFP proteins were categorized during meiosis and ascospore formation. This study unveiled a het-S spore-killing system that is governed by dosage of and interaction between the [Het-s] prion and the HET-S protein. Due to this property of the [Het-s] prion, the het-s allele acts as a meiotic drive element favoring maintenance of the prion-forming allele in natural populations.
Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data

Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
Synaptic physiology of horizontal connections in the cat's visual cortex

Horizontal connections are a principal component of intrinsic cortical circuitry. They arise mainly from pyramidal cells and course parallel to the brain's surface for distances as long as 8 mm, linking columns with shared orientation preference and allowing cells to integrate visual information from outside their receptive fields. We examined the synaptic physiology of the horizontal pathway in slices of the cat's striate cortex and found that activating lateral fibers produced both excitation and inhibition. We recorded the postsynaptic responses of identified pyramidal cells in layer 2 + 3 of area 17 to electrical shocks applied at three sites: in the home column of the impaled neuron either in layer 2 + 3 or 4, or at a lateral distance of 0.9–3 mm in layer 2 + 3. Within the home column, suprathreshold stimuli produced compound EPSPs with action potentials, followed by fast, GABAAergic IPSPs and a slower, GABABergic IPSP. For the distant stimulating site, the threshold response was an EPSP. Stronger shocks frequently evoked a disynaptic, GABAAergic IPSP that truncated the EPSP and could dominate the postsynaptic response. At the resting potential, the horizontally evoked EPSP was too small to elicit spikes. With depolarization of the membrane, however, it grew several hundred-fold. This amplification was blocked by N-(2,6-dimethylphenylcarbamoylmethyl)triethylammonium bromide (QX-314), but not by 2-amino-5-phosphonovalerate (APV), indicating that it was mediated by Na+ channels, rather than by NMDA receptors. We propose that the horizontal connections provide the means for stimuli outside the receptive field to modulate activity elicited within its confines. The voltage-dependent enhancement of the laterally evoked EPSP may explain why stimulating the surround by itself fails to drive cells but can facilitate their response to stimuli within the receptive field. The ability to initiate disynaptic inhibition from lateral sites shows that recruiting appropriate groups of horizontal fibers can also have a suppressive effect. Thus, the effect of horizontal input is state dependent, with the size and sign of the laterally evoked response changing according to the balance of converging inputs.
A memory-based approach to recognizing programming plans

utomated Program understanding can be viewed as the process of automatically extracting design knowledge from source code. Past research efforts have automatically extracted and used this knowledge to restructure programs [4], to tutor novice programmen [5, lo], to ~generate documentation [15, 161, and to locate reusable components [ti, 111. Our interest lies in automatically extracting object-oriented design knowlrdge to support translating C programs to C ++. In particular, we are interested in recognizing common ol$xts and operations in C programs and replacing them with libraries containing human-generated object-oriented code written in C ++. This is an appealing task for automated program understanding for several reasons. First, even if it is possible only to automatically recognize and replace a small portion of the many objects and operations implicitly present in a set of real-world programs , it is a win over attempting to revise these programs entirely by hand. Second, hand translation of C to C ++ requires constructing replacement C ++ classes, so it is not unreasonable to assume that information about C implementations of these classes can be provided while constructing the replacement classes. As an example, consider the problem of translating the C program in Figure 1 into its ot$xt-oriented C ++counterpart in Figure 2. Translating even this simple C program requires understanding its purpose, its design, and the mapping between its design and its implementation. Its purpose is to print the average distance between a set of x, y points. Its design divides into two pieces. One reads pairs of points, computes the distance between them, adds this distance to a running total, and updates a running count. The other calculates the average and prints the result. Its implementation stores point coordinates as separate variables, combines a while loop and a scanf to read the input points, computes the distance using a series of arithmetic operations and assignments, and prints the average using printf and an expression which provides an average of 0 if no values are read. All of this design information is necessary to translate Figure 1 into Figure 2, as the C ++ program has the same general design, but makes explicit that the program is manipulating points, calculating distances, computing averages, and so on. The difficulty is that this design must be inferred from relationships between elements of the source code, as the program is poorly documented and uses uninformative variable names. Our …
Expressing and Addressing Uncertainty: A Study of Collaborative Problem-Solving Dialogues

To support learners during collaborative problem solving, developing a deeper understanding of collaborative dialogue is essential. This paper focuses on one important aspect of collaborative dialogue: expressions of uncertainty. In a study of undergraduate novice computer science students working in pairs, we observed that the students who produced the lowest quality solutions expressed uncertainty more often than those who produced middle-quality solutions. Perhaps surprisingly, pairs with the highest quality solutions also expressed more uncertainty than the middle performers. Examining the ways in which students expressed and then followed up on uncertainty revealed that higherperforming pairs utilized emerging learning opportunities when uncertainty was expressed, and remained focused on one task at a time. In contrast, the lower-performing pairs often did not resolve their uncertainty before moving on, attempting to work with multiple incomplete pieces of the solution simultaneously. These findings provide insight into how best to support collaborative learning during uncertainty.
Medical audit of diabetes mellitus in primary care setting in Bosnia and Herzegovina.

AIM To assess the quality of diabetes care provided by family medicine teams in primary health centers in Bosnia and Herzegovina (BH) through a medical audit, addressing the extent to which clinical practice complied with pre-determined explicit criteria of long-term management. METHOD Retrospective analysis included randomly selected medical records of patients with type 1 or 2 diabetes mellitus treated by 18 family medicine teams at 5 locations in BH, included in the Canadian International Development Agency/World Health Organization project "Strengthening health care systems in BH with focus on primary health care/family medicine model. " Audit record form contained 24 questions on sex, age, diabetes type, body mass index (BMI), hypertension, family anamnesis, annual examinations (HbA1C, BMI, lipid profile or total cholesterol, blood creatinine, neurological examination, urinalysis for albuminuria, foot care, and examination of ocular fundus), smoking habits, alcohol consumption, patient education, prescribed insulin and other drugs, and patient's health care-seeking behavior. Standardized and record forms were returned anonymously with 99.3% response rate. RESULTS Records of 536 patients with diabetes were analyzed (64% women and 87% patients with diabetes mellitus type 2). Family medicine teams showed poor compliance with established criteria for diabetes control. Metabolic control (69.5%) was acceptable, but the level of monitoring complications of diabetes (foot and ocular fundus examined in 53.4% and 53% of patients, respectively) was low. There were also considerable variations in diabetes management between different centers as well as between the teams in the same center. CONCLUSION The audit revealed deficiencies in the quality of diabetes care and variations in care provision between primary care teams. Clinical guidelines and continuing education about acceptable diabetes care should be developed and implemented in BH.
Reconstructing contact network parameters from viral phylogenies

Models of the spread of disease in a population often make the simplifying assumption that the population is homogeneously mixed, or is divided into homogeneously mixed compartments. However, human populations have complex structures formed by social contacts, which can have a significant influence on the rate of epidemic spread. Contact network models capture this structure by explicitly representing each contact which could possibly lead to a transmission. We developed a method based on kernel approximate Bayesian computation (kernel-ABC) for estimating structural parameters of the contact network underlying an observed viral phylogeny. The method combines adaptive sequential Monte Carlo for ABC, Gillespie simulation for propagating epidemics though networks, and a kernel-based tree similarity score. We used the method to fit the Barabási-Albert network model to simulated transmission trees, and also applied it to viral phylogenies estimated from five published HIV sequence datasets. On simulated data, we found that the preferential attachment power and the number of infected nodes in the network can often be accurately estimated. On the other hand, the mean degree of the network, as well as the total number of nodes, were not estimable with kernel-ABC. We observed substantial heterogeneity in the parameter estimates on real datasets, with point estimates for the preferential attachment power ranging from 0.06 to 1.05. These results underscore the importance of considering contact structures when performing phylodynamic inference. Our method offers the potential to quantitatively investigate the contact network structure underlying viral epidemics.
Structured Assessment of Minor Surgical Skills (SAMSS) for Clinical Clerks

The goal of a properly designed surgery clerkship is to support the individual aspirations of all students, and to provide the basic surgical training necessary for all physicians. It is important for all graduating physicians to possess a basic level of skill for the performance of technical procedures. It is therefore important that the students leave their undergraduate surgical rotations with appropriate levels of technical skill regardless of their anticipated practice paths. Many clinical nonsurgical fields have become more invasive and procedure-oriented, making use of technical skill on a regular basis. Residents in nonsurgical fields are therefore in need of some of the same technical skill training as surgical residents. Ideally the best time to acquire basic technical skills is in the clerkship. However, little information is available showing whether or not undergraduate surgical rotations prepare students sufficiently to meet technical skills objectives. In order to assess whether technical skills are developed sufficiently in clerkship, a reliable and valid evaluation of these technical skills is required. Technical skill evaluation has been studied in postgraduate trainees. The Objective Structured Assessment of Technical Skill (OSATS) was developed for the appraisal of technical skill in surgical trainees. The OSATS platform consisted of surgical trainees rotating among skill stations while being evaluated by surgeons using checklists and global rating scales. This examination has been demonstrated to be statistically reliable while satisfying many important validity issues. A similar evaluation tool has been developed for the assessment of technical skill in family practice residents. This Structured Assessment of Minor Surgical Skill (SAMSS) has been shown to have moderate to high reliability and show evidence of construct validity. The skills tested were different between the two examinations, reflecting the specific task and skill expectations of the surgical and family practice residents. Since many of the procedures that clinical clerks should be performing are considered minor surgical procedures, the SAMSS format may be directly applicable to this group of trainees. However, since medical students differ from residents due to their heterogeneous career aspirations, aptitudes, and skill expectations, it is important to demonstrate that the SAMSS is a valid and reliable assessment of technical skill in clerkship prior to generalizing the SAMSS to the medical student arena.