Miracle-dz/UniFAR-FTUs huggingface dataset:
Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets

High-Throughput technologies provide genomic and trascriptomic data that are suitable for biomarker detection for classification purposes. However, the high dimension of the output of such technologies and the characteristics of the data sets analysed represent an issue for the classification task. Here we present a new feature selection method based on three steps to detect class-specific biomarkers in case of high-dimensional data sets. The first step detects the differentially expressed genes according to the experimental conditions tested in the experimental design, the second step filters out the features with low discriminative power and the third step detects the class-specific features and defines the final biomarker as the union of the class-specific features. The proposed procedure is tested on two microarray datasets, one characterized by a strong imbalance between the size of classes and the other one where the size of classes is perfectly balanced. We show that, using the proposed feature selection procedure, the classification performances of a Support Vector Machine on the imbalanced data set reach a 82% whereas other methods do not exceed 73%. Furthermore, in case of perfectly balanced dataset, the classification performances are comparable with other methods. Finally, the Gene Ontology enrichments performed on the signatures selected with the proposed pipeline, confirm the biological relevance of our methodology. The download of the package with the implementation of Peculiar Genes Selection, ‘PGS’, is available for R users at: http://github.com/mbeccuti/PGS.
Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non‐canonical mechanisms may be employed. The rod‐shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.
DNA‐damage processing in blood lymphocytes of head‐and‐neck‐squamous‐cell‐carcinoma patients is dependent on tumor site

It has been reported that an intrinsic susceptibility to cancer is related to the way an individual responds to DNA‐damaging agents. The aim of this study was to evaluate whether, in addition to bleomycin‐induced chromosomal instability, radiation‐induced initial DNA damage and subsequent repair is associated with the development of head‐and‐neck squamous‐cell carcinoma. In this study, 2 assays were performed to measure DNA damage in human peripheral‐blood lymphocytes. One was a chromosomal aberration assay which determines sensitivity to chromatid breaks induced by bleomycin, the other an elegant immunochemical assay which measures the level of radiation‐induced strand breaks as well as subsequent repair. Age, smoking and alcohol‐drinking behavior did not influence the number of chromatid breaks, initial DNA damage or repair capacity. As has been found in previous studies, the mean number of chromatid breaks per cell was significantly different between patients (n = 18) and control persons (n = 19), whereas the amount of initial DNA damage was not. No correlation was found between the outcome of the 2 assays in the subject groups. In contrast to laryngeal‐carcinoma patients, oral‐cavity‐carcinoma patients showed significantly slower repair capacity than controls. Our hypothesis is that the way DNA damage is processed by the patients determines at which site cancer develops in the head and neck area. © 1996 Wiley‐Liss, Inc.
Call Me “Tiger”: Ernest S. Burch, Jr., the Smithsonian, and Remembrance

Ernest Burch’s long and varied career spanning the circumpolar Arctic began with excursions to Labrador, Greenland, and Newfoundland in 1954, 1959, and 1962. His initiation into arctic anthropology through the mentorship of Elmer Harp, Jr., his later collaboration with the Smithsonian Handbook Project, and his Research Associate appointment with the Arctic Studies Center created much common ground with the Smithsonian. This paper reviews Burch’s career-long relationship with the Smithsonian Institution and through a short personal memorial he wrote in 2010 for Elmer Harp’s Memorial reveals the beginning of his career.
Le déclin des centres-villes : mythe ou réalité? Analyse comparative des régions métropolitaines nord-américaines.

Pour les grandes villes nord-americaines, de nombreuses etudes confirment le deplacement des activites economiques vers la banlieue. Devons-nous pour autant sonner le glas des centres-villes et de la centralite? Apres avoir effectue une revue des travaux sur le sujet, nous analysons 32 regions metropolitaines pour la periode 1980-1995, en postulant que la force du centre-ville se revelera dans les rapports de prix centre/banlieue pour les espaces a bureau. Nous n'observons pas de tendance generalisee de declin des centres villes. Les prix demeurent, en regle generale, plus eleves au centre, meme s'il existe des poles secondaires forts. Nous observons des differences importantes d'une ville et d'une region a l'autre, notamment entre villes canadiennes et americaines.
Deep hashing for large-scale image retrieval

In recent years, because of its ability to improve the retrieval efficiency and reduce the storage space, the image hashing methods based on deep learning have got widely attention in large-scale image retrieval system. At first, this paper introduces the development of the deep learning network, and analyzes the advantages and disadvantages of the deep hashing methods combined with convolutional network and hashing algorithm in current trend. And then it summarizes the research status of the traditional hashing, compares the deep hashing methods and the traditional hashing, points out the great potential of the large-scale image retrieval technology based on the deep hashing. Finally, combined with the existing hashing learning framework based on deep convolution neural network, we put forward some suggestions.
Immunohistochemical analysis of cyclooxygenase (COX)‐2 expression in pancreatic endocrine tumors: Association with tumor progression and proliferation

An immunohistochemical study of cyclooxygenase (COX)‐2 expression in pancreatic endocrine tumors (PET) was carried out, and the expression of COX‐2 was compared with pathological features, the expression of several markers (hormones, vascular endothelial growth factor, single‐stranded DNA, and the Ki‐67 labeling index [LI]). Twenty PET, including 10 metastasizing cases (tumor size: 3–8 cm) and 10 non‐metastasizing cases (tumor size: 0.3– 8 cm) were studied. Tumors with a high level of COX‐2 expression were placed in the H group, and the remaining tumors were placed in the L group. The H group was comprised of 13 tumors: all 10 of the metastasizing cases and three of the non‐metastasizing cases. There were significant differences in tumor size between the two groups (H group 46.5 mm; L group 0.9 mm). There were significant differences in the presence of the following histological criteria for malignancy: pleomorphism (H group 13/13; L group 1/7), mitotic activity (H group 2.9; L group 0) and/or angioinvasion (H group 13/13; L group 1/7); and there were also significant differences in the number of cases that expressed ectopic hormones (gastrin, vasoactive intestinal peptide, serotonin and calcitonin; H group 12/13; L group 2/7) and in the Ki‐67 LI (H group 8.3%; L group 0.4%). The distribution of COX‐2‐positive cells tended to be similar to the distribution of Ki‐67‐positive cells. Our data show that COX‐2 is frequently upregulated in malignant PET and that there is a close relationship between COX‐2 expression and tumor progression / proliferative activity.
Evolution of Ig DNA Sequence to Target Specific Base Positions Within Codons for Somatic Hypermutation1

Ig variable (V) region genes are subjected to a somatic hypermutation process as B lymphocytes participate in immune reactions to protein Ags. Although little is known regarding the mechanism of mutagenesis, a consistent hierarchy of trinucleotide target preferences is evident. Analysis of trinucleotide regional distributions predicted and we now empirically confirm the surprising finding that the framework 2 region of κ V region genes is highly mutable despite its importance to the structural integrity and function of the Ab molecule. Interestingly, much of this mutability appears to be focused on the third codon position where synonymous substitutions are most likely to occur. We also observed a trend for high predicted mutability for codon positions 1 and 2 in complementarity-determining regions. Consequently, amino acid replacements should occur at a higher rate in complementarity-determining regions than in framework regions due to the distribution and subsequent targeting of microsequences by the mutation mechanism. Our results reveal a subtle tier of V region gene evolution in which DNA sequence has been molded to direct mutations to specific base positions within codons in a manner that minimizes damage and maximizes the benefits of the somatic hypermutation process.
Performance Analysis of Gray Code based Structured Regular Column-Weight Two LDPC Codes

The Low-Density Parity-Check (LDPC) code is a linear block code specified by a parity-check matrix H. The construction process of LDPC codes considers the parameters such as row weight, column weight, density of H-matrix, code rate, code length and girth. A novel flexible method for constructing structured regular LDPC codes considering all these parameters, using Gray-code representations, was reported in our earlier work. LDPC codes with column-weight two have low computational complexity and are promising for data storage and partial response channels. This paper presents the performance analysis of column-weight two LDPC codes constructed using the method proposed in our previous work. The BER performance of the obtained codes is comparable to that of the standard Gallager"s random codes and QC-LDPC codes.
Centrifugal force induced by relativistically rotating spheroids and cylinders

Starting from the gravitational potential of a Newtonian spheroidal shell we discuss electrically charged rotating prolate spheroidal shells in the Maxwell theory. In particular we consider two confocal charged shells which rotate oppositely in such a way that there is no magnetic field outside the outer shell. In the Einstein theory we solve the Ernst equations in the region where the long prolate spheroids are almost cylindrical; in equatorial regions the exact Lewis ‘rotating cylindrical’ solution is so derived by a limiting procedure from a spatially bound system. In the second part we analyze two cylindrical shells rotating in opposite directions in such a way that the static Levi-Civita metric is produced outside and no angular momentum flux escapes to infinity. The rotation of the local inertial frames in flat space inside the inner cylinder is thus exhibited without any approximation or interpretational difficulties within this model. A test particle within the inner cylinder kept at rest with respect to axes that do not rotate as seen from infinity experiences a centrifugal force. Although in suitably chosen axes the spacetime there is exactly Minkowskian out to the inner cylinder, nevertheless, those inertial frame axes rotate with respect to infinity, so relative to the inertial frame inside the inner cylinder a test particle is traversing a circular orbit.
Comb-Based RF Photonic Filters Based on Interferometric Configuration and Balanced Detection

We demonstrate a novel technique to improve radio frequency (RF) performance such as RF gain and noise figure (NF) for comb-based RF photonic filters. While conventional RF photonic links use a dual-output modulator and balanced detection, this RF photonic filter utilizes an interferometric configuration with double sideband suppressed carrier modulation and balanced detection. This technique can simultaneously provide filter tunability, 6-dB RF gain increase, and noise cancellation. The RF gain and NF of the RF photonic filter are improved to approximately 0 and 24 dB, respectively. With the improved RF performance, we perform the tuning of the filter center frequencies from 2 to 8 GHz with no baseband filter response (<;-38 dB), no RF power fading, while maintaining good filter shape (sidelobe suppression and stopband attenuation >32 dB).
Selective IGT decision-making impairment in a patient with juvenile Parkinson's disease and pathological gambling: A role for dopaminergic therapy?

The orbitofrontal cortex and the dopaminergic system are structures involved in managing impulsivity and sensibility to reinforcements, and both are typically impaired in Parkinson's disease (PD). Also, l-DOPA treatment can contribute to the development of the ‘Dopamine Dysregulation Syndrome’, a syndrome that can influence the patients' personality and lead to risk-taking behaviors. In this study, we describe the case of a 42-year-old woman (LT) affected by juvenile PD, treated with both l-DOPA and dopamine agonists, who showed a sudden onset of pathological gambling (PG), as the only neuropsychiatric symptom. We assessed LT with a full neuropsychological battery and the Iowa Gambling Task (IGT), in order to describe her specific failure in decision making. LT's performance on the IGT is compared with that of 15 non-demented PD patients under therapy with dopamine agonists and no behavioral dysregulations and with that of 16 age- and education-matched healthy subjects. Results showed fully preserved memory, executive functions, and reasoning abilities for LT, but a remarkable and stable impairment in the IGT. Performance of LT on the IGT is significantly lower than that of both control groups. This case shows, for the first time, that high cognitive functioning and preserved executive functions are no guarantee for advantageous decision making, and that the onset of PG is consistent with selective orbitofrontal disruption and side-effects of dopamine agonist therapy. It is also showed that the IGT is a useful neuropsychological device to detect specific risk-taking behaviors, which compromise functioning in real life.
Low drug resistance to both platinum and taxane chemotherapy on an in vitro drug resistance assay predicts improved survival in patients with advanced epithelial ovarian, fallopian and peritoneal cancer

The objective of this study was to evaluate the role of an in vitro drug resistance assay to platinum and taxane in the management of advanced epithelial ovarian, fallopian and primary peritoneal cancer. All patients with FIGO Stage IIIc and IV who received postoperative chemotherapy with platinum and taxane for more than 4 courses after the initial cytoreductive surgery between 1995 and 2008 were evaluated. Patients who received neoadjuvant chemotherapy were not included. An in vitro drug resistance assay (EDR Assay, Oncotech, Tustin, CA) was used to determine drug resistance for each patient's tumor tissue. Level of drug resistance was described as extreme (EDR), intermediate (IDR), or low (LDR). Response to chemotherapy and survival were correlated to the EDR Assay. Of the 335 patients who underwent primary cytoreductive surgery, 173 cases met the criteria for statistical evaluation. The 58 patients (33.5%) whose tumors had LDR to both platinum and taxane had statistically improved progression‐free survival and overall survival (OS) compared with the 115 patients (66.5%) who demonstrated IDR or EDR to platinum and/or taxane (5‐year OS rates, 41.1% vs. 30.9%, p = 0.014). The 5‐year OS rates for the 28 (16.2%) cases that had optimal cytoreduction with LDR to both platinum and taxane was significantly improved over the 62 (35.8%) cases that were suboptimally cytoreduced with IDR or EDR to platinum and/or taxane (54.1% vs. 20.4%, respectively, p < 0.001). In conclusion, LDR to both platinum and taxane chemotherapy, as determined by an in vitro drug resistance assay, independently predicts improved survival in patients with advanced epithelial ovarian, fallopian and peritoneal cancer, especially in those patients who undergo optimal primary cytoreduction. © 2009 UICC
Natural environments, obesity, and physical activity in nonmetropolitan areas of the United States.

PURPOSE To assess the associations of the natural environment with obesity and physical activity in nonmetropolitan areas of the United States among representative samples by using 2 indices of outdoor activity potential (OAP) at the county level. METHODS We used the data from 457,820 and 473,296 noninstitutionalized adults aged over 18 years for obesity and physical activity, respectively, from the 2000-2006 Behavioral Risk Factor Surveillance System. The OAP indices were (1) a recreational opportunity index based on 24 variables related to outdoor physical activity, such as the number of facilities available for walking, biking, hiking, and swimming derived from the 1997 National Outdoor Recreation Supply Information System; and (2) a natural amenities index which was based on physical and social environmental characteristics, such as climate, topographic relief, land cover, and tourism. We fitted logistic regression models using generalized estimating equations to control for county level intracorrelation and tested each index separately to assess its relationship with obesity and physical activity. FINDINGS Recreational opportunities were higher in areas with greater natural amenities. After controlling for individual-level socioeconomic and demographic characteristics, the prevalence of obesity decreased and propensity for physical activity increased with increasing levels of both recreational opportunities and natural amenities. CONCLUSIONS Multiple indices of OAP based on characteristics of the built, natural and social environments were associated with decreased obesity and increased physical activity in nonmetropolitan areas. Public health interventions should consider the opportunities and limitations offered by the natural environment for promoting physical activity and reducing obesity in rural areas.
The Non-Optimality of Proposed Monetary Policy Rules Under Timeless-Perspective Commitment

Several recent papers have usefully emphasized the inefficiency that arises from discretionary monetary policymaking, relative to optimal policy from a 'timeless perspective,' in macroeconomic models with forward-looking private behavior. The inefficiency in question is in terms of average outcomes of the conditional expectation of a policy objective that reflects the discounted present value of current and future period losses (which involve squared deviations of inflation and output from specified target levels). In the literature, most of the analysis has been conducted in an optimizing model that features a Calvo-Rotemberg price adjustment equation that includes a 'cost-push' shock term. This literature suggests that policy, which keeps inflation equal to a negative multiple of the change in the output gap, is optimal with respect to the criterion mentioned above -- the unconditional expectation of the policymaker's objective function. Results reported here show, however, that this is not the case -- that an alternative policy rule, suggested by the approach of 'policy design' rather than by 'optimal control,' delivers superior results.
The tubulin code at a glance

ABSTRACT Microtubules are key cytoskeletal elements of all eukaryotic cells and are assembled of evolutionarily conserved α-tubulin–β-tubulin heterodimers. Despite their uniform structure, microtubules fulfill a large diversity of functions. A regulatory mechanism to control the specialization of the microtubule cytoskeleton is the ‘tubulin code’, which is generated by (i) expression of different α- and β-tubulin isotypes, and by (ii) post-translational modifications of tubulin. In this Cell Science at a Glance article and the accompanying poster, we provide a comprehensive overview of the molecular components of the tubulin code, and discuss the mechanisms by which these components contribute to the generation of functionally specialized microtubules. Summary: In this Cell Science at a Glance article and accompanying poster, we present the basic building blocks of the tubulin code.
Smooth variable structure observer controller with adaptive gains: Application to robot manipulators control

In this paper, an observer based controller is developed, both of them working in sliding mode, applied to the square MIMO non-linear systems control. An application to the rigid robots with n links and n revolute joints (n-degree of freedom) is presented. In order to reduce the chattering, a parameterised smooth switching function is used: the tangent hyperbolic function both in the observer and controller. The gain of the switching functions is adaptively updated, depending on the state estimation error and tracking error, respectively. Using the adaptive gains, the transient and tracking response are improved. Closed loop simulations with a 2-degree of freedom robot manipulator, in the presence of parameter uncertainties, are presented in order to show the robustness of the approach.
Form and Function of Mortuary Architecture: The Middle and Late Bronze Age Tomb Complex at Ashkelon

Abstract Traditional interpretations of the form and function of mortuary architecture have tended to focus on status, gender and age, with, for example, larger, more elaborate tombs being assumed to have housed an individual(s) of high social status. The Middle and Late Bronze Age chamber tombs of Canaan, are often perceived as multi-generational family tombs, and are thought to have belonged to extended family groups, probably of high social and economic status. Although the labour-intensive architectural form of chamber tombs may be an indicator of status, their function as a 'family tomb' is often overlooked. Upon close scrutiny, the confusing mix of intertwined burials may reveal intra-family organization. Rather than simply random burials, these deposits may represent intentional clustering for the purpose of identifying smaller familial groups within the larger kinship group who shared the tomb. If this is true, such clustering would underscore the importance of burial with one's own kin, demonstrate intra-family relationships, and preserve the integrity of the smaller family group.