Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and analysis of key genes in osteosarcoma using bioinformatics

Osteosarcoma (OS) is an invasive malignant neoplasm of the bones. The present study identified and analyzed key genes associated with OS. Expression profiling of the dataset GSE49003, which included 6 metastatic and 6 non-metastatic OS cell lines and was obtained from the Gene Expression Omnibus, was performed. Following data preprocessing, the differentially expressed genes (DEGs) were selected using the limma package in R. Subsequently, bidirectional hierarchical clustering using the pheatmap package in R and an unpaired Students' t-test was performed for the DEGs. Based on the Search Tool for the Retrieval of Interacting Genes database and Cytoscape software, a protein-protein interaction (PPI) network for the DEGs was constructed. Using Database for Annotation, Visualization and Integrated Discovery software and the Kyoto Encyclopedia of Genes and Genomes Orthology Based Annotation System server, functional and pathway enrichment analyses were performed for the DEGs corresponding to the proteins of the network. In addition, the transcription factors (TFs) and CpG islands of the gene promoter were searched for using the TRANSFAC database and CpG Island Searcher software, respectively. A total of 323 DEGs were identified between the metastatic and non-metastatic samples. In the PPI network, upregulated epidermal growth factor receptor (EGFR) exhibits a high degree and was therefore highly interconnected with other proteins. Enrichment analysis revealed that EGFR was enriched in cytoskeleton organization, organic substance response and the signaling pathway of focal adhesion. The TFs early growth response 1, nuclear factor-κB complex subunits, peroxisome proliferator activated receptor α, signal transducer and activator of transcription 3 and MYC proto-oncogene were identified in the EGFR promoter region. Furthermore, multiple CpG islands, starting from the 400 bp of the EGFR promoter sequence, were predicted. Methylated modification of the CpG islands in the EGFR promoter may help to regulate EGFR expression. The TFs identified in the EGFR promoter may function in the progression of OS.
Macular Ganglion Cell Complex Reduction Preceding Visual Field Loss in a Patient With Chiasmal Compression With a 21-Month Follow-Up: Comment.

were calculated in a circular fashion, according to the Early Treatment Diabetic Retinopathy Study, but rotated (45 ) to provide quadrantic measurements respecting the vertical and horizontal meridians. After excluding the fovea, values were calculated for the inner and outer segments of each quadrant. A comparison of the first and last OCT measurements showed RGC-IPL reduction in the 4 nasal quadrantic measurements ranging from 11% to 34.5%, right eye, and from 12.2% to 25.3%, left eye. A small percentage thickness reduction was also found in the temporal inner segments bilaterally (Table 1). Several studies evaluating patients with VF defects from chiasmal compression have shown that peripapillary RNFL thickness and macular RGC layer thickness are significantly correlated with VF loss on SAP (4–8) and that patients with less structural damage experience greater visual improvement after chiasmal decompression (5–7). In many patients, VF improvement, despite persistent retinal structural damage, may be attributed to restoration of transmission of neuronal impulses in axons that remain viable (2). This had led to the concept that in compressive optic pathway lesions, functional VF loss precedes structural loss, a rationale challenged by the findings of Tieger et al (1). Our patient's preference for conservative management made it possible to compare VF and OCT data prospectively over an almost 2-year (21-month) follow-up period. There was mild deterioration of the VFs over this time period, yet OCT data (especially RGC-IPL thickness) displayed definite worsening in both eyes. Horton (2) suggested that the conventional size III target used in SAP may not be sensitive enough to detect subtle VF loss. The VF results in our patient support this, as the field loss was only well defined using size I (0.25 mm2), I/2e, and I/1e targets on careful GP in the right eye. Also, it is important to notice that even on GP, progressive visual loss was not clearly defined, despite definite reduction of the RGC layer in the left eye. Therefore, it is likely that in chronic compressive lesions, retinal structures are impaired before clinically detectable VF loss. Our findings suggest that structural retinal measurements in addition to VF testing are a useful aid in the diagnosis and follow-up of patients with compressive lesions of the anterior visual pathway. Mário Luiz Ribeiro Monteiro, MD, PhD Division of Ophthalmology (MLRM), University of São Paulo Medical School, São Paulo, Brazil
Modelling fuzzy partitions with fuzzy answer sets

This paper introduces a representation of fuzzy partitions in terms of fuzzy logic programming. This representation models relationships among the different classes that define the fuzzy partition. There are essentially two such relationships. The first one is that classes are disjoint and, therefore, contradictory each other; on the other hand, the second one is that classes cover all the universe. These two relationships are modeled via two different negations, namely, the explicit and default negation. Last but not least, the semantics used to model both negations is the fuzzy answer set semantics.
Kinesigenic dystonia as the first manifestation of multiple sclerosis with cervical and brainstem lesions.

Paroxysmal symptoms, particularly paroxysmal dystonia (also referred to as ‘tonic seizure’), had been clearly related to multiple sclerosis (MS) by Matthews [1] in 1958, although such symptoms had been reported since 1928 [2]. Sometimes they may be the first manifestation of the demyelinating disease [3]. When they occur without other signs or symptoms they often present diagnostic difficulties. We describe the case of a young man with laboratory-supported definite MS [4] in whom unilateral tonic spasms were the initial symptom. A 27-year old man was admitted with a history of variable numbness affecting the right side of his body, beginning 2 months earlier; 1 month later he developed carpope-dal spasms in his right hand and sometimes a dystonic involvement of his lower right limb, facial grimacing, torsion of the neck and dysarthria. The episodes lasted about 60s and were not accompanied by an alteration in consciousness, loss of sphincter control or postictal sequels. During the dystonic posturing a Babinski sign was present on the right side. Such episodes occurred 4-5 times daily only during the waking-up period. They were always evoked by voluntary movements of the neck or of the right arm and by hyperventilation (while the patient was at rest, but not if he blew into a bag). On admission physical examination disclosed brisk muscle stretch reflexes on the right, slight impairment of vibratory sensation in the right upper limb. Plantar re-
Surface–Specific Electrical Occlusal Caries Diagnosis: Reproducibility, Correlation with Histological Lesion Depth, and Tooth Type Dependence

Electrical conductance measurements are being used experimentally for occlusal caries detection. Recently, it was suggested to cover the fissure system with a conducting medium, resulting in a surface–specific measurement. It was the aim of this study to determine in vitro the reproducibility of this modified technique for occlusal caries in posterior teeth, to determine for a large study sample the correlation between the electrical measurements and histological lesion depth, and to evaluate the difference between results for premolars and molars. For the reproducibility determination, surface–specific electrical resistance measurements were made using a sample of 68 posterior teeth. Eight operators performed measurements on all teeth, and repeated measurements on 24 teeth. The validity study included the previous sample and the collected samples from two more studies, resulting in a total sample of 325 posterior teeth. One operator had performed electrical resistance measurements on all teeth in the sample. Reproducibility was good: mean Pearson's correlation coefficient 0.89 (±0.05) for interexaminer correlation, and 0.86 (±0.12) for intra–examiner correlation, using log (resistance) as the result parameter. The correlation coefficient between log(resistance) and histological lesion depth for the large sample was –0.78 for all teeth, –0.64 for premolars, and –0.73 for molars. The regression line for molars was located below the regression line for premolars: at a hypothetical histology score of 2.5 (a dentine caries threshold) the estimated resistance threshold would be 507 kΩ for premolars, and 233 kΩ for molars. Converted to Electronic Caries Monitor (ECM) readings, the difference is about 1.4 on the ECM scale. It was concluded that the in vitro reproducibility of the described surface–specific method for electrical resistance measurement is very good, even for inexperienced operators. The correlation between measurements and histological lesion depth is moderate to good. The method is sensitive to electrode area differences, which will result in different clinical cut–offs for caries diagnosis in premolar and molar teeth.
Growth Hormone, Fatigue, Poor Sleep, and Disability in HIV Infection

Poor sleep, daytime fatigue, and loss of cognitive ability exist during all stages of HIV infection, worsening with disease progression. These symptoms contribute to disability and poor quality of life. Data from several research groups support a role of somnogenic inflammatory process peptides elevated in HIV infection, e.g. TNFα. Though the literature is in conflict regarding an effect of HIV infection on growth hormone (GH) secretion, GH axis dysregulation and treatment with GH may be important in HIV infection, e.g. in the wasting syndrome. It has long been known that GH varies with changes in sleep. The hypothesis tested in the current study was that the relationship between delta frequency (0.5–4.0 Hz) sleep EEG amplitude (square root of power from frequency analysis) and GH secretion would differ between HIV positive (HIV+) and HIV negative (HIV–) subjects. In 14 subjects (6 HIV+ and 8 HIV–, none with current or past AIDS-defining illness) a linear relationship change across the night’s sleep was found in the coupling between delta frequency sleep EEG amplitude and GH secretion. The phase coupling change was in opposite directions in HIV+ versus HIV– subjects. This difference supports the hypothesis that the brain-based coordination of sleep and sleep-related physiology deteriorates early in HIV infection, and that GH dysregulation may contribute to this sleep pathology.
Comparative analysis of k-nearest neighbor and modified k-nearest neighbor algorithm for data classification

Data mining is the process of handling information from a database which is invisible directly. Data mining is predicted to become a highly revolutionary branch of science over the next decade. One of data mining techniques is classification. The most popular classification technique is K-Nearest Neighbor (KNN). But there is also the Modified K-Nearest Neighbor (MKNN) classification algorithm which is the derived algorithm of KNN. In this paper we will analyze the comparison of KNN and MKNN algorithms to classify the data of Conditional Cash Transfer Implementation Unit (Unit Pelaksana Program Keluarga Harapan) which consist of 7395 records. Comparative analysis is based on the accuracy of both algorithms. Before classification, K-Fold Cross Validation was done to search for the optimal data modeling resulted in data modeling on cross 2 with accuracy of 93.945%. The results of K-Fold Cross Validation modeling will be the model for training data samples and testing data to test KNN and MKNN for classification. Classification result produced accuracy based on the rules of confusion matrix. The test resulted in the highest accuracy of KKN by 94.95% with average accuracy during the test was 93.94% and the highest accuracy of MKNN was 99.51% with the average accuracy during the test was 99.20%, almost all testing from the first test up to the tenth, MKNN algorithm is superior and has better accuracy value than KNN so it can be analyzed that the ability of MKNN algorithm in accuracy is better than KNN. It can be concluded that MKNN algorithm is capable of handling accuracy better for classification than KNN algorithm, by ignoring other aspects such as computerization, time efficiency, and algorithm effectiveness.
Impact of Nephron–Sparing Surgery on Quality of Life in Patients with Localized Renal Cell Carcinoma

Objectives: The aim of the study is to evaluate the impact of nephron–sparing surgery on postoperative quality of life (QOL) in patients with localized renal cell carcinoma, compared with radical nephrectomy. Methods: From 1986 to 1996, a total of 66 patients with localized small renal cell carcinoma <4 cm in diameter and a functioning contralateral renal unit underwent radical nephrectomy (n = 51) or nephron–sparing surgery (n = 15). Of these, 50 patients evaluated various dimensions of QOL using standardized self–rating questionnaires, EORTC QLQ–C30. Results: There is no significant difference in 5–year overall survival between the nephron–sparing surgery group and the radical nephrectomy group. With regard to postoperative QOL, patients who underwent nephron–sparing surgery showed a significantly higher score on physical function than patients treated with radical nephrectomy (p<0.05). Nephron–sparing surgery was additionally superior to radical nephrectomy in terms of fatigue, sleep disturbance, pain and constipation. Conclusion: Selected patients with localized, small, unilateral renal cell carcinoma and a normal contralateral kidney will benefit from nephron–sparing surgery.
Variation in Residential Care Community Resident Characteristics, by Size of Community: United States, 2016.

Residents of residential care communities are persons who cannot live independently but generally do not require the skilled care provided by nursing homes. On any given day in 2016, an estimated 811,500 residents were in residential care communities (1,2). As the population ages, the numbers in residential care communities will likely increase, creating a sizeable group within the long-term care population. This report presents national estimates of selected characteristics of residential care community residents in 2016 and compares them by community size. State-level estimates are available from:
Parametric joint modelling for longitudinal and survival data

Joint modelling is the simultaneous modelling of longitudinal and survival data, while taking into account a possible association between them. A common approach in joint modelling studies is to assume that the repeated measurements follow a lin- ear mixed e�ects model and the survival data is modelled using a Cox proportional hazards model. The Cox model, however, requires a strong proportionality assump- tion, which seems to be violated quite often. We, thus, propose the use of parametric survival models. Additionally, joint modelling literature mainly deals with right- censoring only and does not consider left-truncation, which can cause bias. The joint model proposed here considers left-truncation and right-censoring.
Etiketa-lainoen Ikuskera Hobetzeko Multzokatzea

Laburpena: Erabiltzaileek aurrez anotatutako datuak berreskuratzeko baliabide interesgarria bilakatu dira markatzaile sozialak. Mota honetako webguneek etiketarik erabilienek osatutako etiketa-lainoa erakusten dute nabigazio aukera gisa. Etiketalaino hauek, ordea, ez dute etiketen arteko antzekotasuna ez eta edukia kontuan izaten. Lan honetan SOM mapak erabiliz etiketen arteko erlazioak definitzeko metodoa aurkezten dugu. Erlazio hauek definitzeko, web dokumentuen edukietan oinarritu gara. Emaitza bezala lortutako mapa, ondorioz, etiketa-multzo ezberdinez osatzen da, multzo horietako bakoitzean termino esanguratsuenak erakutsiz nabigazioa eta ikuskera hobetzen direlarik. Azkenik, metodologia honek izan dezakeen aplikazio erreala aztertzen dugu. Hitz gakoak: markatzaile sozialak, etiketak, etiketa-lainoa, multzokatzea
Clinical Factors Influencing the Performance of Gene Expression Classifier Testing in Indeterminate Thyroid Nodules.

BACKGROUND Molecular diagnostic testing is increasingly used in the management of indeterminate thyroid nodules. Limited data exist regarding the influence of clinical factors on gene expression classifier (GEC) test performance. This study examined the positive and negative predictive value of GEC as stratified by nodule size. METHODS A prospectively maintained pathology database from a single tertiary referral center was queried from 2012 to 2015 for indeterminate thyroid nodules that underwent GEC testing. Nodule size, patient demographics, Bethesda classification, and Hürthle cell-predominant nodules (HCNs) were evaluated as predictors of GEC performance. RESULTS Two hundred and thirty-one patients with 245 indeterminate nodules were examined. Assuming all nodules to be benign unless proven malignant on histopathology, the sensitivity and specificity of GEC testing were 95.2% and 60.1%, respectively. The malignancy rate among resected nodules was 25.3%. The positive predictive value was consistent across nodule sizes: 45.5% for nodules <1 cm, 42.9% for nodules 1-1.9 cm, 36.0% for nodules 2-2.9 cm, 54.2% for nodules 3-3.9 cm, and 50.0% for nodules ≥4 cm. The negative predictive value ranged from 93.3% to 100% and was not affected by nodule size. HCNs had a high rate of GEC suspicious results (77.4% vs. 50.5% for nodules without Hürthle cell predominance, p < 0.01), though this did not correspond to a difference in the rate of malignancy (25.8% vs. 25.3%). CONCLUSIONS Nodule size did not affect GEC test performance in the present cohort. GEC benign results remain reliable in large nodules. GEC suspicious nodules >3 cm carry a similar risk of malignancy compared to smaller nodules, and do not warrant more aggressive treatment. GEC testing has limited clinical utility for HCNs due to the high rate of false-positive results.
Speech Sound Representation, Perception, and Plasticity: A Neurophysiologic Perspective

Historically, auditory research has focused predominately upon how relatively simple acoustic signals are represented in the neuronal responses of the auditory periphery. However, in order to understand the neurophysiology underlying speech perception, the ultimate objective is to discover how speech sounds are represented in the central auditory system and to relate that representation to the perception of speech as a meaningful acoustic signal. This paper reviews three areas that pertain to the central auditory representation of speech: (1) the differences in neural representation of speech sounds at different levels of the auditory system; (2) the relation between the representation of sound in the auditory pathway and the perception/misperception of speech, and (3) the training-related plasticity of speech sound neural representation and speech perception.
Moment-to-moment changes in feeling moved match changes in closeness, tears, goosebumps, and warmth: time series analyses

ABSTRACT Feeling moved or touched can be accompanied by tears, goosebumps, and sensations of warmth in the centre of the chest. The experience has been described frequently, but psychological science knows little about it. We propose that labelling one’s feeling as being moved or touched is a component of a social-relational emotion that we term kama muta (its Sanskrit label). We hypothesise that it is caused by appraising an intensification of communal sharing relations. Here, we test this by investigating people’s moment-to-moment reports of feeling moved and touched while watching six short videos. We compare these to six other sets of participants’ moment-to-moment responses watching the same videos: respectively, judgements of closeness (indexing communal sharing), reports of weeping, goosebumps, warmth in the centre of the chest, happiness, and sadness. Our eighth time series is expert ratings of communal sharing. Time series analyses show strong and consistent cross-correlations of feeling moved and touched and closeness with each other and with each of the three physiological variables and expert-rated communal sharing – but distinctiveness from happiness and sadness. These results support our model.
Predictive Significance of Magnetic Resonance Imaging at 4 Months of Adjusted Age in Infants after a Perinatal Neurologic Insult

The aim of this prospective study was to evaluate the predictive significance of magnetic resonance imaging (MRI) performed at 4 months of corrected age in 60 neonates after a perinatal neurologic insult. Follow-up ranged from 2 to 5 years of chronological age. MRI examination was normal in 10; isolated external hydrocephalus was found in 15 infants. Twenty-three of these infants developed normally. Focal or multifocal lesions were shown in 6 infants, of whom 2 developed normally. Diffuse brain involvement was present in 29 cases as atrophy (n = 18), leukomalacia (n = 5), basal ganglia lesions (n = 3), and delayed myelination (n = 3). All but 4 infants showed neurologic impairment. MRI performed at 4 months of adjusted age is of prognostic significance in neonates who suffer a moderate or mild neurologic insult.
miR-200b-3p in plasma is a potential diagnostic biomarker in oral squamous cell carcinoma

Abstract Context: Circulating MicroRNAs (miRNAs) are emerging as novel biomarkers for tumour. Objective: Evaluate the diagnostic potential of plasma miR-200b-3p in oral squamous cell carcinoma (OSCC). Materials and methods: miR-200b-3p was detected by qRT-PCR in paired pre-operative and post-operative plasmas from 80 OSCC patients and 80 healthy controls. Results: Plasma miR-200b-3p was significantly upregulated in OSCC, and it was higher in WHO II/III grade than WHO I grade. The AUC of miR-200b-3p for OSCC was 0.9173. miR-200b-3p was significantly downregulated after surgery. High miR-200b-3p expression was associated with poor prognosis. Discussion and conclusion: Plasma miR-200b-3p could be a potential diagnostic biomarker for OSCC.
Mapping the spatiotemporal dynamics of processing task‐relevant and task‐irrelevant sound feature changes using concurrent EEG‐fMRI

The cortical processing of changes in auditory input involves auditory sensory regions as well as different frontoparietal brain networks. The spatiotemporal dynamics of the activation spread across these networks has, however, not been investigated in detail so far. We here approached this issue using concurrent functional magnetic resonance imaging (fMRI) and electroencephalography (EEG), providing us with simultaneous information on both the spatial and temporal patterns of change‐related activity. We applied an auditory stimulus categorization task with switching categorization rules, allowing to analyze change‐related responses as a function of the changing sound feature (pitch or duration) and the task relevance of the change. Our data show the successive progression of change‐related activity from regions involved in early change detection to the ventral and dorsal attention networks, and finally the central executive network. While early change detection was found to recruit feature‐specific networks involving auditory sensory but also frontal and parietal brain regions, the later spread of activity across the frontoparietal attention and executive networks was largely independent of the changing sound feature, suggesting the existence of a general feature‐independent processing pathway of change‐related information. Task relevance did not modulate early auditory sensory processing, but was mainly found to affect processing in frontal brain regions. Hum Brain Mapp 37:3400–3416, 2016. © 2016 Wiley Periodicals, Inc.