Assessment of deep learning algorithms to predict histopathological diagnosis of breast cancer: first Moroccan prospective study on a private dataset.

OBJECTIVE: Breast cancer is a critical public health issue and a leading cause of cancer-related deaths among women worldwide. Its early diagnosis and detection can effectively help in increasing the chances of survival rate. For this reason, the diagnosis and classification of breast cancer using Deep learning algorithms have attracted a lot of attention. Therefore, our study aimed to design a computational approach based on deep convolutional neural networks for an efficient classification of breast cancer histopathological images by using our own created dataset. We collected overall 328 digital slides, from 116 of surgical breast specimens diagnosed with invasive breast carcinoma of non-specific type, and referred to the histopathology department of the National Institute of Oncology in Rabat, Morocco. We used two models of deep neural network architectures in order to accurately classify the images into one of three categories: normal tissue-benign lesions, in situ carcinoma or invasive carcinoma. RESULTS: Both Resnet50 and Xception models achieved comparable results, with a small advantage to Xception extracted features. We reported high degrees of overall correct classification accuracy (88%), and sensitivity (95%) for detection of carcinoma cases, which is important for diagnostic pathology workflow in order to assist pathologists for diagnosing breast cancer with precision. The results of the present study showed that the designed classification model has a good generalization performance in predicting diagnosis of breast cancer, in spite of the limited size of the data. To our knowledge, this approach can be highly compared with other common methods in the automated analysis of breast cancer images reported in literature.

Whole-Genome Sequencing of Two Moroccan Mycobacterium tuberculosis Strains.

Mycobacterium tuberculosis is known to cause pulmonary and extrapulmonary tuberculosis. In Morocco, the spread of multidrug-resistant (MDR) tuberculosis (TB) has become a major challenge. Here, we announce the draft genome sequences of two Mycobacterium tuberculosis strains, MTB1 and MTB2, isolated from patients with pulmonary tuberculosis in Morocco, to describe variants associated with drug resistance.

Growth, morphology and electronic properties of epitaxial graphene on vicinal Ir(332) surface.

Superlattice induced minigaps in graphene band structure due to underlying one-dimensional nanostructuration has been demonstrated. A superperiodic potential can be introduced in graphene if the substrate is periodically structured. The successful preparation of a periodically nanostructured substrate in large scale can be obtained by carefully studying the electronic structure with a spatial averaging technique such as high-energy resolution photoemission. In this work, we present two different growth methods such as temperature programmed growth (TPG) and chemical vapor deposition (CVD) studied by scanning tunnelling microscopy (STM) and low energy electron diffraction (LEED). In both methods, we show that the original steps of Ir(332) have modified with (111) terraces and step bunching after graphene growth. Graphene grows continuously over the terrace and the step bunching areas. We observe that while TPG growth does not give rise to a well-defined surface periodicity required for opening a bandgap, the CVD growth does. By combining with angle-resolved photoemission spectroscopy (ARPES) measurements, we correlate the obtained spatial periodicity to observed band gap opening in graphene.

Gastric Adenocarcinoma in a Moroccan Population: First Report on Survival Data.

BACKGROUND: Although its incidence has decreased over the last 20 years, gastric adenocarcinoma remains frequent (1,033,701 new cases worldwide per year, Globocan 2018). Its prognosis is still poor, with overall survival rates of 10 to 25% despite improvement in surgical and perioperative treatment. In Morocco, we do not have data on survival and predictors of mortality in our population, the present study aims to describe the epidemiological and clinicopathological features of gastric adenocarcinoma and the survival rate. MATERIALS AND METHODS: We retrospectively reviewed data files of 265 patients with histological diagnosis of gastric adenocarcinoma between January 2007 and June 2017. Survival was estimated by the Kaplan Meier method and prognostic factors in multivariate analysis (Cox model). RESULTS: The mean age of our population was 54.48 ±15.53 with a sex ratio M/F of 1.76. Clinical symptomatology dominated by epigastralgia episodes in two-thirds of the cases and deterioration of the general state in most cases (61.7%). Proximal localization accounted for 17.4%. According to histological classification, poorly differentiated adenocarcinoma was the most common histological type (51.7%). Metastatic or locally advanced tumors accounted for 92% of cases. Only 11% of patients received curative resection. The 5-year survival was 6%. Multivariate analysis revealed three prognostic factors: vascular invasion, advanced stage and differentiation. DISCUSSION: The high mortality of gastric adenocarcinoma in our Moroccan series is probably explained by the late stage at diagnosis. Symptoms are nonspecific and endoscopy is usually performed for advanced symptoms such as anemia, bleeding or weight loss. The main identified prognostic factors in gastric adenocarcinoma are tumor subtype (Linitic forms), stage at diagnosis, vascular and lymph nodes invasion and general performance status which correlates to available data in the literature. Besides, the age distribution of GC in our series showed that the proportion of affected young adult is high (30.6%) compared to data from developed countries varying between 6 and 15%. This age distribution can be explained by the Westernization of diet, the increase of obesity in our population and more exposure to alcohol and tobacco. CONCLUSION: Overall cancer survival in our population does not exceed 7%, a rate that remains low compared to studies published in the occidental literature. Recommendations have to be elaborated to make a strategy for screening and early diagnosis of gastric adenocarcinoma to improve the survival rate.

Stroke and syphilis: A retrospective study of 53 patients.

OBJECTIVE: The aim of this study was to describe the clinical, biological and radiological characteristics of patients with syphilitic vasculitis, and to assess the outcome after treatment. METHODOLOGY: A retrospective review was carried out based on the records of patients with ischemic stroke, and reactive CSF TPHA and VDRL results. None of these patients showed symptoms of any other diseases or had received high doses of penicillin. RESULTS: A total of 53 patients with stroke met the diagnostic criteria for syphilitic arteritis. Their average age was 41±12 years. Nine patients had a history of genital ulcer (17%), and the median duration of illness after presenting a chancre was 8 [range: 1-14] years. A prodromal syndrome was seen in 27 patients (50.9%) and included changes in mental status in 14 patients (26.4%), seizures in 10 cases (18.9%), headache in eight (15.1%) and memory loss in seven (13.2%). Neurological events included focal motor deficits in 29 cases (54.7%), ataxia in 11 (20.8%) and movement disorders in 15 (28.3%). HIV serology was performed in 31 patients and proved negative in every case. Disease evolution was generally favorable: 12 patients (22.6%) were autonomous at the time of hospital discharge; 29 (54.7%) had partially recovered; and only seven (13.2%) still had signs of severe sequelae. CONCLUSION: A diagnosis of syphilitic stroke should be suspected in young patients as a manifestation of syphilis, and tests for neurosyphilis should be routine in neurology departments to make a prompt diagnosis, thereby preventing psychological sequelae.

Epidemiology of viral hepatitis in the Maghreb.

INTRODUCTION: Viral hepatitis represents a serious public health problem in the world especially in the Maghreb where the prevalence of the 5 viruses A, B, C, D, and E remains high and varies from one Maghreb country to another, there is few published studies on these infections in our Maghreb countries. METHOD OF STUDY: Our work is a review of the literature about prevalence, the most common mode of transmission, and the most exposed population for these viruses in the Maghreb countries through published studies between 2011 and 2017. RESULT: It has been found that the Maghreb countries are endemic for the five viruses with variable prevalence from one country to another, with sometimes heterogeneous data in the same country. For hepatitis B, Mauritania is the Maghreb country most affected by this infection unlike the rest of the Maghreb countries which are moderately endemic for this virus, the lowest prevalence of VHB was noted in Morocco, the genotype the most common is the D for the majority of Maghreb countries, and the precore mutant profile is also the most common. For hepatitis C the prevalence of infection does not vary much from one Maghreb country to another, but it remains slightly higher in Mauritania. The population most exposed to the virus C in the five countries is hemodialysis patients. The most common genotype in all Maghreb countries is genotype 1 except for Libya, where genotype 4 remains the most common probably related to its borders with Egypt. For hepatitis D, Mauritania is the only Maghreb country with a high endemicity for the virus. Tunisia has the lowest prevalence for hepatitis A and E compared to the rest of the Maghreb countries, all of which are endemic for these two viruses with fecal-oral transmission. CONCLUSION: The management of these viral hepatitis is costly for the health economy and to reduce their prevalence, prevention measures must be followed like vaccination and improving hygiene conditions.

Annotated Whole-Genome Shotgun Sequence of Multidrug-Resistant Mycobacterium tuberculosis MTB13_M Isolated from Morocco.

Here, we describe the annotated genome sequence of Mycobacterium tuberculosis MTB13_M. The organism was isolated from a sputum sample in Morocco.

Anticandidal, antibacterial, cytotoxic and antioxidant activities of Calendula arvensis flowers.

Calendula arvensis (CA) is one of the important plants used in traditional medicine in Morocco, due to its interesting chemical composition. The present study aimed to determine the anticandidal, antioxidant and antibacterial activities, and the effects of extracts of CA flowers on the growth of myeloid cancer cells. Also, to characterize the chemical composition of the plant. Flowers of CA were collected based on ethnopharmacological information from the villages around the region Rabat-Khemisset, Moroccco. The hexane and methanol extracts were obtained by soxhlet extraction, while aqueous extracts was obtained by maceration in cold water. CA extracts were assessed for antioxidant activity using four different methods (DPPH, FRAP, TEAC, ß-carotene bleaching test). Furthermore, the phenolic and flavonoid contents were measured, also the antimicrobial activity has been evaluated by the well diffusion method using several bacterial and fungal strains. Finally, extracts cytotoxicity was assessed using MTT test. Phytochemical quantification of the methanolic and aqueous extracts revealed that they were rich with flavonoid and phenolic content and were found to possess considerable antioxidant activities. MIC values of methanolic extracts were 12.5-25µg/mL. While MIC values of hexanolic extracts were between 6.25-12.5µg/mL and were bacteriostatic for all bacteria while methanolic and aqueous extracts were bactericidal. In addition, the extracts exhibited no activity on Candida species except the methanolic extract, which showed antifungal activity onCandida tropicalis 1 and Candida famata 1. The methanolic and aqueous extracts also exhibited antimyeloid cancer activity (IC50 of 31µg/mL). In our study, we conclude that the methanolic and aqueous extracts were a promising source of antioxidant, antimicrobial and cytotoxic agents.

Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C.

Here, we report the draft genome sequences of methicillin-susceptible Staphylococcus captis pulsotype NCRS-C (CR02 strain) and multiresistant Staphylococcus captis pulsotype NCRS-A (CR07 strain).

Spin to Charge Conversion at Room Temperature by Spin Pumping into a New Type of Topological Insulator: α-Sn Films.

We present results on spin to charge current conversion in experiments of resonant spin pumping into the Dirac cone with helical spin polarization of the elemental topological insulator (TI) α-Sn. By angle-resolved photoelectron spectroscopy (ARPES), we first check that the Dirac cone (DC) at the α-Sn (0 0 1) surface subsists after covering Sn with Ag. Then we show that resonant spin pumping at room temperature from Fe through Ag into α-Sn layers induces a lateral charge current that can be ascribed to the inverse Edelstein effect by the DC states. Our observation of an inverse Edelstein effect length much longer than those generally found for Rashba interfaces demonstrates the potential of TIs for the conversion between spin and charge in spintronic devices. By comparing our results with data on the relaxation time of TI free surface states from time-resolved ARPES, we can anticipate the ultimate potential of the TI for spin to charge conversion and the conditions to reach it.

Wide geographical dissemination of the multiresistant Staphylococcus capitis NRCS-A clone in neonatal intensive-care units.

Nosocomial late-onset sepsis represents a frequent cause of morbidity and mortality in preterm neonates. The Staphylococcus capitis clone NRCS-A has been previously described as an emerging cause of nosocomial bacteraemia in French neonatal intensive-care units (NICUs). In this study, we aimed to explore the possible unrecognized dissemination of this clone on a larger geographical scale. One hundred methicillin-resistant S. capitis strains isolated from neonates (n = 86) and adult patients (n = 14) between 2000 and 2013 in four different countries (France, Belgium, the UK, and Australia) were analysed with SmaI pulsed-field gel electrophoresis (PFGE) and dru typing. The vast majority of NICU strains showed the NRCS-A pulsotype and the dt11c type (96%). We then randomly selected 14 isolates (from neonates, n = 12, three per country; from adult patients, n = 2), considered to be a subset of representative isolates, and performed further molecular typing (SacII PFGE, SCCmec typing, and multilocus sequence typing-like analysis), confirming the clonality of the S. capitis strains isolated from neonates, despite their distant geographical origin. Whole genome single-nucleotide polymorphism-based phylogenetic analysis of five NICU isolates (from the different countries) attested to high genetic relatedness within the NRCS-A clone. Finally, all of the NRCS-A strains showed multidrug resistance (e.g. methicillin and aminoglycoside resistance, and decreased vancomycin susceptibility), with potential therapeutic implications for infected neonates. In conclusion, this study represents the first report of clonal dissemination of methicillin-resistant coagulase-negative Staphylococcus clone on a large geographical scale. Questions remain regarding the origin and means of international spread, and the reasons for this clone's apparent predilection for neonates.

Semiconducting Graphene from Highly Ordered Substrate Interactions.

While numerous methods have been proposed to produce semiconducting graphene, a significant band gap has never been demonstrated. The reason is that, regardless of the theoretical gap formation mechanism, subnanometer disorder prevents the required symmetry breaking necessary to make graphene semiconducting. In this work, we show for the first time that semiconducting graphene can be made by epitaxial growth. Using improved growth methods, we show by direct band measurements that a band gap greater than 0.5 eV can be produced in the first graphene layer grown on the SiC(0001) surface. This work demonstrates that order, a property that remains lacking in other graphene systems, is key to producing electronically viable semiconducting graphene.

Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units.

Staphylococcus capitis pulsotype NRCS-A was previously reported as a frequent cause of late-onset sepsis in neonatal intensive care units (NICUs) worldwide. Here, we report the whole-genome shotgun sequences of four S. capitis pulsotype NCRS-A strains, CR03, CR04, CR05, and CR09, isolated from Belgium, Australia, the United Kingdom, and France, respectively.

Ultrafast Atomic Diffusion Inducing a Reversible (2sqrt[3]×2sqrt[3])R30°â†”(sqrt[3]×sqrt[3])R30° Transition on Sn/Si(111)∶B.

Dynamical phase transitions are a challenge to identify experimentally and describe theoretically. Here, we study a new reconstruction of Sn on silicon and observe a reversible transition where the surface unit cell divides its area by a factor of 4 at 250 °C. This phase transition is explained by the 24-fold degeneracy of the ground state and a novel diffusive mechanism, where four Sn atoms arranged in a snakelike cluster wiggle at the surface exploring collectively the different quantum mechanical ground states.

Articular fracture of the base of the thumb metacarpal: Comparative study between direct open fixation and extrafocal pinning.

The treatment of intra-articular fractures of the base of the first metacarpal bone should aim to anatomically reduce the articular surface, restore the initial length of the first metacarpal and preserve the opening of the first web space. These objectives appear to be achievable with a well-conducted surgical treatment. In a retrospective study, we reviewed a series of 38 cases, which compared open reduction and internal fixation (ORIF) and extrafocal pinning to determine which option provided the best reduction and functional recovery in young, manual workers. Direct fixation was better at restoring the configuration of the joint, regardless of the age and sex of the patients and the fracture type. This complete reduction is associated clinically with better function. Thumb opposition was statistically better in fractures treated by ORIF. Thumb retroposition was better in the cases treated by ORIF, but not significantly. ORIF appears the best technique for treating intra-articular fractures of the base of the first metacarpal, as it results in better functional recovery.

Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A).

Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the human microflora. Recently, a clonal population of Staphylococcus capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis (LOS) in several neonatal intensive care units in France. Here, we report the complete genome sequence and annotation of the prototype Staphylococcus capitis NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids) exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA genes and 4 rRNA genes.

Tuning a Schottky barrier in a photoexcited topological insulator with transient Dirac cone electron-hole asymmetry.

The advent of Dirac materials has made it possible to realize two-dimensional gases of relativistic fermions with unprecedented transport properties in condensed matter. Their photoconductive control with ultrafast light pulses is opening new perspectives for the transmission of current and information. Here we show that the interplay of surface and bulk transient carrier dynamics in a photoexcited topological insulator can control an essential parameter for photoconductivity-the balance between excess electrons and holes in the Dirac cone. This can result in a strongly out of equilibrium gas of hot relativistic fermions, characterized by a surprisingly long lifetime of more than 50 ps, and a simultaneous transient shift of chemical potential by as much as 100 meV. The unique properties of this transient Dirac cone make it possible to tune with ultrafast light pulses a relativistic nanoscale Schottky barrier, in a way that is impossible with conventional optoelectronic materials.

Two-dimensional electron gas with six-fold symmetry at the (111) surface of KTaO3.

Two-dimensional electron gases (2DEGs) at transition-metal oxide (TMO) interfaces, and boundary states in topological insulators, are being intensively investigated. The former system harbors superconductivity, large magneto-resistance, and ferromagnetism. In the latter, honeycomb-lattice geometry plus bulk spin-orbit interactions lead to topologically protected spin-polarized bands. 2DEGs in TMOs with a honeycomb-like structure could yield new states of matter, but they had not been experimentally realized, yet. We successfully created a 2DEG at the (111) surface of KTaO3, a strong insulator with large spin-orbit coupling. Its confined states form a network of weakly-dispersing electronic gutters with 6-fold symmetry, a topology novel to all known oxide-based 2DEGs. If those pertain to just one Ta-(111) bilayer, model calculations predict that it can be a topological metal. Our findings demonstrate that completely new electronic states, with symmetries not realized in the bulk, can be tailored in oxide surfaces, promising for TMO-based devices.

Nature of the bad metallic behavior of Fe1.06Te inferred from its evolution in the magnetic state.

We investigate with angle-resolved photoelectron spectroscopy the changes of the Fermi surface and the main bands from the paramagnetic state to the antiferromagnetic (AFM) state occurring below 72 K in Fe1.06Te. The evolution is completely different from that observed in Fe pnictides, as nesting is absent. The AFM state is a rather good metal, in agreement with our magnetic band structure calculation. On the other hand, the paramagnetic state is very anomalous with a large pseudogap of ~65 meV on the electron pocket that closes in the AFM state. We discuss this behavior in connection with spin fluctuations existing above the magnetic transition and the correlations predicted in the spin-freezing regime of the incoherent metallic state.