Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement of c-axis angular orientation in calcite (CaCO3) nanocrystals using X-ray absorption spectroscopy

We demonstrate that the ability to manipulate the polarization of synchrotron radiation can be exploited to enhance the capabilities of X-ray absorption near-edge structure (XANES) spectroscopy, to include linear dichroism effects. By acquiring spectra at the same photon energies but different polarizations, and using a photoelectron emission spectromicroscope (PEEM), one can quantitatively determine the angular orientation of micro- and nanocrystals with a spatial resolution down to 10 nm. XANES-PEEM instruments are already present at most synchrotrons, hence these methods are readily available. The methods are demonstrated here on geologic calcite (CaCO3) and used to investigate the prismatic layer of a mollusk shell, Pinctada fucata. These XANES-PEEM data reveal multiply oriented nanocrystals within calcite prisms, previously thought to be monocrystalline. The subdivision into multiply oriented nanocrystals, spread by more than 50°, may explain the excellent mechanical properties of the prismatic layer, known for decades but never explained.
Waves and instabilities in rotating free surface flows

The stability properties of the rotating free surface flow in a cylindrical container is studied using a global stability approach, considering successively three models. For the case of solid body rotation (Newton’s bucket), all eigenmodes are found to be stable, and are classified into three families: gravity waves, singular inertial modes, and Rossby waves. For the case of a potential flow, an instability is found. The mechanism is explained as a resonance between gravity waves and centrifugal waves, and is thought to be at the origin of the “rotating polygon instability” observed in experiments where the flow is driven by rotation of the bottom plate (see L. Tophoj, J. Mougel, T. Bohr, D. Fabre, The Rotating Polygon Instability of a Swirling Free Surface Flow, Phys. Rev. Lett. 110 (2013) 194502). Finally, in the case of the Rankine vortex which in fact consists in the combination of the two first cases, we report a new instability mechanism involving Rossby and gravity waves.
Mutation of the PIK3CA Gene in Ovarian and Breast Cancer

Phosphatidylinositol 3′-kinases are lipid kinases with important roles in neoplasia. Recently, a very high frequency of somatic mutations in PIK3CA has been reported among a large series of colorectal cancers. However, the relevance of PIK3CA mutation in other cancer types remains unclear because of the limited number of tumors investigated. We have screened a total of 284 primary human tumors for mutations in all coding exons of PIK3CA using a combination of single stranded conformational polymorphism and denaturing high-performance liquid chromatography analysis. Among 70 primary breast cancers, 40% (28 of 70) harbored mutations in PIK3CA, making it the most common mutation described to date in this cancer type. Mutations were not associated with histologic subtype, estrogen receptor status, grade or presence of tumor in lymph nodes. Among the primary epithelial ovarian cancers only 11 of 167 (6.6%) contain somatic mutations, but there was a clear histologic subtype bias in their distribution. Only 2 of 88 (2.3%) of serous carcinomas had PIK3CA mutations compared with 8 of 40 (20.0%) endometrioid and clear cell cancers, which was highly significant (P = 0.001). In contrast, PIK3CA gene amplification (>7-fold) was common among all histologic subtypes (24.5%) and was inversely associated with the presence of mutations. Overall, PIK3CA mutation or gene amplification was detected in 30.5% of all ovarian cancers and 45% of the endometrioid and clear cell subtypes. Our study is the first direct evidence that PIK3CA is an oncogene in ovarian cancer and greatly extends recent findings in breast cancer.
Engineering nanostructured selective layers for reverse osmosis membranes

A major challenge to communities across the world in the next century will be ensuring millions have access to adequate freshwater resources. Studies from the UN World Health Organization indicate that over 1.1 billion people currently lack access to reliable and secure freshwater supplies, with an estimated 2.5 million deaths per year from diseases associated with poor access and sanitation in 2007. Reverse osmosis (RO), a process through which water is desalted via pressurized flow past a salt-selective membrane, is an energy-efficient method to generate freshwater from oceanic, brackish, and waste water sources. However, there are a number of challenges to scaling up RO processes to large scale production, including the need to improve membrane selectivity and throughput. One method to assemble selective layers for RO membranes is layer-by-layer (LbL) assembly, which is a flexible, scalable assembly technique that enables the incorporation of a myriad of polyelectrolytes and inorganic nanoparticles into thin films. There is a gap in the scientific literature concerning the use of LbL to generate RO selective layers where previous approaches have not taken full advantage of the LbL process to incorporate nanomaterials that can generate ordered nanostructures for salt rejection. In particular, high-aspect ratio clay platelets are ideal for such a purpose; it was hypothesized that effective salt rejection could be achieved by hindering the diffusion of solvated ions through nano-channels formed by the platelets embedded within a polymer matrix. This body of work examines the application of spray layer-by-layer (spray-LbL) assembly with clay composite thin film architectures to generate nanostructured selective layers for use in RO membrane technology. First, appropriate substrates were identified as support layers for the deposition of spray- LbL assembled clay composite thin films. Both electrospun bisphenol-A polysulfone (PSU) mats of varying fiber diameter and polyethersulfone (PES) ultrafiltration (UF) membranes with varying pore diameters were examined. Second, a range of materials were investigated for the spray-LbL deposition of clay composite films. Laponite clay platelets were incorporated into several different film architectures including strong polyelectrolytes as well as cross-linkable weak polyelectrolytes to form both bilayer and tetralayer film architectures. The clay content was controlled via manipulating assembly conditions such as the pH and spray times of the film components. Assembled membrane architectures were tested at industrial RO operating conditions in dead-end permeation cells and evaluated for salt rejection, water permeability, and mechanical strength. Ultimately, it was determined the most uniform and robust films were those deposited on PES membranes with 30 nm pores, closely matching the characteristic length of the LAP clay platelets to reduce the impact of bridging. Although all the film architectures tested exhibited significantly greater water permeability than commercially…
Natural history of viral markers in children infected with human T lymphotropic virus type I in Jamaica.

PURPOSE We conducted a longitudinal analysis of human T lymphotropic virus type I (HTLV-I) viral markers in 28 Jamaican mothers and their children, who were monitored for a median of 6.2 years after the birth of the children. METHODS The HTLV-I provirus DNA load was measured using the Taqman system (PE Applied Biosystems). The HTLV-I antibody titer was determined using the Vironstika HTLV-I/II Microelisa System (Organon Teknika). The HTLV-I Tax-specific antibody titers were measured using an enzyme-linked immunosorbent assay. Generalized estimating equations were used to describe the associations of exposure variables with sequentially measured levels of HTLV-I viral markers in children. RESULTS The HTLV-I antibody titer increased significantly up to 1 year after infection, reaching equilibrium at a median titer of 1 : 7,786. The prevalence of Tax-specific antibody reached 80% at 2 years after infection. The provirus load increased up to 2 years after infection, reaching equilibrium at a median of 6,695 copies/100,000 peripheral blood mononuclear cells. The increase in the provirus load was significant only among children with eczema, but not among children without eczema. CONCLUSIONS The provirus loads in children increased for an additional year after their antibody titers had stabilized, possibly as a result of the expansion of HTLV-I-infected clones. This effect was significant only for children with eczema. Among HTLV-I-infected children, eczema may be a cutaneous marker of the risk of HTLV-I-associated diseases developing in adulthood.
On the Optimal Convergence Probability of Univariate Estimation of Distribution Algorithms

In this paper we obtain bounds on the probability of convergence to the optimal solution for the compact genetic algorithm (cGA) and the population based incremental learning (PBIL). Moreover, we give a sufficient condition for convergence of these algorithms to the optimal solution and compute a range of possible values for algorithm parameters at which there is convergence to the optimal solution with a predefined confidence level.
Clique-based cooperative multiagent reinforcement learning using factor graphs

In this paper, we propose a clique-based sparse reinforcement learning (RL) algorithm for solving cooperative tasks. The aim is to accelerate the learning speed of the original sparse RL algorithm and to make it applicable for tasks decomposed in a more general manner. First, a transition function is estimated and used to update the Q-value function, which greatly reduces the learning time. Second, it is more reasonable to divide agents into cliques, each of which is only responsible for a specific subtask. In this way, the global Q-value function is decomposed into the sum of several simpler local Q-value functions. Such decomposition is expressed by a factor graph and exploited by the general maxplus algorithm to obtain the greedy joint action. Experimental results show that the proposed approach outperforms others with better performance.
Shallow Updates for Deep Reinforcement Learning

Deep reinforcement learning (DRL) methods such as the Deep Q-Network (DQN) have achieved state-of-the-art results in a variety of challenging, high-dimensional domains. This success is mainly attributed to the power of deep neural networks to learn rich domain representations for approximating the value function or policy. Batch reinforcement learning methods with linear representations, on the other hand, are more stable and require less hyper parameter tuning. Yet, substantial feature engineering is necessary to achieve good results. In this work we propose a hybrid approach -- the Least Squares Deep Q-Network (LS-DQN), which combines rich feature representations learned by a DRL algorithm with the stability of a linear least squares method. We do this by periodically re-training the last hidden layer of a DRL network with a batch least squares update. Key to our approach is a Bayesian regularization term for the least squares update, which prevents over-fitting to the more recent data. We tested LS-DQN on five Atari games and demonstrate significant improvement over vanilla DQN and Double-DQN. We also investigated the reasons for the superior performance of our method. Interestingly, we found that the performance improvement can be attributed to the large batch size used by the LS method when optimizing the last layer.
Modified adriamycin‐vincristine‐dexamethasone (m‐VAD) in primary refractory and relapsed plasma cell myeloma: an NCI (Canada) pilot study

Summary. The purpose of this single arm phase II study was to test a modified version of the three drug combination vincristine, adriamycin and dexamethasone (m‐VAD), in which intravenous vincristine (0·4 mg/d) and adriamycin (9 mg/m2 per day) infusions are administered for only 2 h on days 1–4 of each 28 d cycle, in patients with refractory multiple myeloma. In addition, only two 4 d courses of dexamethasone 40 mg/d was given during each cycle. The entry criteria for 44 patients included plasma cell myeloma and a measurable monoclonal peak, either refractory to initial treatment with melphalan and prednisone, or resistant to melphalan and prednisone after initially responding (resistant relapsed disease, 27 patients). Patients treated previously with chemotherapy other than melphalan and predisone were excluded. There were no complete responses. Of the 41 evaluable patients who completed at least one course of therapy 11 had a partial response (27%, 95% C.I. 14–40%). The response rates were 19% for primary refractory disease patients, and 32% for those with resistant relapsed disease. The median duration of response was 4 months. The median survival for all 44 patients was 7·6 months (5·5 months for primary refractory patients, and 10 months for relapsed resistant disease patients). Episodes of documented bacterial infection occurred in 12 patients, and 10 patients had minor viral infection. The dexamethasone dose was reduced in 12 patients. The median neutrophil nadir was 1·2 × 109/l, and median platelet nadir was 147 × 109/l. Five deaths were judged as treatment related and occurred during marrow cytopenia. The results of this modified form of VAD are inferior to that reported previously for 4 d continuous infusions of vincristine and doxorubicin. This could be related to either patient selection factors, or to a reduction of the efficacy of the drug combination produced by either the shortened intravenous infusions and/or omission of one 4 d course of dexamethasone.
Multiple idiopathic external apical root resorption: A rare case report

Multiple idiopathic external apical root resorption (MIEARR) is a relatively rare condition affecting multiple teeth in a dentition. As the condition is nonsymptomatic, a case is usually detected as an incidental radiographic finding. However, it may cause pain and mobility in severe cases. It is sometimes self-limiting or sometimes may progress to tooth loss. This paper presents a case of external apical root resorption involving multiple teeth in which etiology was not identified, so idiopathic root resorption was considered as a diagnosis of exclusion.
Reduced telomere length is not associated with early signs of vascular aging in young men born after intrauterine growth restriction: a paradox?

Objective: The mechanisms that increase cardiovascular risk in individuals born small for gestational age (SGA) are not well understood. Telomere shortening has been suggested to be a predictor of disease onset. Our aim was to determine whether impaired intrauterine growth is associated with early signs of vascular aging and whether telomere length could be a biomarker of this pathway. Methods: One hundred and fourteen healthy young men born SGA or after normal pregnancy [appropriate for gestational age (AGA)] were enrolled. Patient data were gathered from questionnaires and clinical exams, including blood pressure (BP) measurement routine laboratory analyses, and carotid intima–media thickness (cIMT). Leukocyte telomere length (LTL) was assessed by quantitative PCR. Birth data were obtained from medical records. Results: The SGA group had significantly higher pulse pressure and cIMT, and a trend to increased SBP and heart rate in comparison to the AGA group. Interestingly, SGA men exhibited a 42% longer LTL than the AGA group. LTL was inversely associated with age, BMI, BP and birth parameters. In multiple regression analysis, BMI was the key determinant of SBP and cIMT. Conclusion: Young men born SGA show early signs of vascular aging. Unexpectedly, in our cohort, the SGA group had longer telomeres than the normal controls. Although longer telomeres are predictive of better health in the future, our findings could indicate a faster telomere attrition rate and probable early onset of cardiovascular risk in SGA participants. Follow-up of this cohort will clarify hypothesis and validate telomere dynamics as indicators of future health risks.
The influence of meniscectomy and ovariectomy on the ovine anterior cruciate ligament

Current research supports a link between osteoarthritis (OA) and the decline in oestrogen levels at menopause. It is not known whether altered hormone levels exert their effect primarily on articular cartilage, or whether associated degeneration of other oestrogen-responsive joint tissues such as cruciate ligaments may significantly contribute. This study investigated the influence of ovariectomy and/or the presence of concurrent osteoarthritis (bilateral meniscectomy model) on the fibrillar structure of collagen within the anterior cruciate ligament (ACL). Sheep (n=24) were treated experimentally with one or more of the following treatments: ovariectomy (OVX), meniscectomy (MENX) or non-operated control (NOC). ACLs were examined using transmission and scanning electron microscopy (TEM & SEM), gene expression, biochemical analysis and histology. TEM studies showed OVX and MENX affect collagen fibril size and arrangement, while the combination of prior OVX and concurrent osteoarthritis (MENX) produced a different pattern of derangement to either treatment alone and may indicate a synergistic effect. Observed structural changes complemented molecular findings of altered mRNA expression, and changes in the collagen and sulphated glycosaminoglycan content of ACL tissue. This study demonstrates that ovariectomy significantly affects ACL collagen fibril structure, and influences the response of the ACL to surgical OA (MENX). These results show the potential for changes in ACL structure post-menopause to influence joint integrity.
Physiological organization of layer 4 in macaque striate cortex

Numerous highly angled electrode penetrations through the opercular region of macaque striate cortex reveal that layers 4A, 4C alpha, and 4C beta--the primary input sublaminae for axons from the lateral geniculate nucleus (LGN)--are retinotopically organized on a fine scale and populated mostly by monocularly driven cells having small receptive fields and lacking orientation selectivity. Layer 4B, which does not receive a direct thalamic input, contains orientationally selective cells, and many of these are also direction selective. To a significant degree the response properties of cells in layers 4C alpha and 4C beta reflect the response properties of their respective afferent inputs, from the magno- and parvocellular laminae of the LGN. Accordingly, cells in layer 4C alpha have lower contrast thresholds and larger minimum response fields than do the cells in layer 4C beta. In contrast to this clear-cut separation, the cells of layer 4A (whose major source of direct LGN input arises from the parvocellular layers) exhibit both high and low contrast thresholds. With regard to the precision of retinotopic mapping that is seen in lamina 4C, it is noteworthy that there is substantial overlap among the minimum response fields of neighboring neurons. Due to a larger mean receptive field size, this overlap is greater in layer 4C alpha than it is in 4C beta. In either sublamina, however, the minimum cortical distance that separates different and nonoverlapping parts of the visual field corresponds closely--within a factor of 2--to the known arborizational spreads of single geniculate afferents.
Pathogenic characteristics of persistent feline enteric coronavirus infection in cats

Feline coronaviruses (FCoV) comprise two biotypes: feline enteric coronaviruses (FECV) and feline infectious peritonitis viruses (FIPV). FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. FIPV arises from FECV by mutation. FCoV also occur in two serotypes, I and II, of which the serotype I viruses are by far the most prevalent in the field. Yet, most of our knowledge about FCoV infections relates to serotype II viruses, particularly about the FIPV, mainly because type I viruses grow poorly in cell culture. Hence, the aim of the present work was the detailed study of the epidemiologically most relevant viruses, the avirulent serotype I viruses. Kittens were inoculated oronasally with different doses of two independent FECV field strains, UCD and RM. Persistent infection could be reproducibly established. The patterns of clinical symptoms, faecal virus shedding and seroconversion were monitored for up to 10 weeks revealing subtle but reproducible differences between the two viruses. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The implications of our results, particularly our insights into the persistently infected state, are discussed.
Spatial Queueing Processes

This study introduces a spatial queueing model for stochastic service systems in which customers or units move about and receive services in a region or a general space. The state of the system at any time is a point process that describes the numbers of units in subsets of the space, and the point process evolves over time as a Markov process. The system may be closed or open with a finite or unlimited capacity, and there may be multiple types of customers. The main result is a closed form expression for the stationary distribution of a spatial queueing process. Sufficient conditions are given for the process to be ergodic. Further results include formulas for throughputs, Little laws for average waiting times in sectors of the space, and necessary and sufficient conditions for various flows in open systems to be Poisson processes in time and space. Examples are given of systems with sector-dependent service rates, local-regional service rates, and multiclass customers. A large family of spatial systems are multi-class queueing networks in which the customer classes are nondiscrete marks or quantities e.g., resources for services, temperature, physical characteristics that affect services and routings.