Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale Expansion of Human Stem and Progenitor Cells From Bone Marrow Mononuclear Cells in Continuous Perfusion Cultures

There is a growing consensus that clinical practice in the areas of bone marrow (BM) transplantation and gene therapy will rely on the ex vivo expansion of hematopoietic cells. We report here on the development of continuously perfused culture systems (bioreactor systems) that expand human stem and progenitor cells from BM mononuclear cell (MNC) populations obtained without cell enrichment. In three separate experiments, 10 bioreactors were each inoculated with 3 x 10(7) BM MNC from patients undergoing marrow harvest for autologous transplantation. At various times thereafter (between days 6 and 16), duplicate bioreactors were harvested and cells were analyzed. The bioreactors contained three cell populations that were analyzed separately: nonadherent cells; cells that were loosely adherent to the endogenously formed stromal layer; and an adherent cell layer that required trypsinization for removal. Total cell numbers increased continuously to give an overall 10-fold (range, 8- to 11-fold) expansion by day 14. The adherent stromal layer significantly expanded to more than 2 x 10(7) cells, but remained less than 6% of the total cell population. Colony-forming unit-granulocyte-macrophage (CFU-GM) numbers expanded 21-fold (range, 12- to 34-fold) by day 14 and, because this expansion was greater than that for total cells, CFU-GM were enriched by as much as fourfold by day 14. Burst-forming unit-erythroid (BFU-E) numbers peaked earlier than did CFU-GM numbers, with a 12-fold (range, 6- to 18-fold) expansion obtained on day 8. In contrast to CFU- GM, which were predominantly nonadherent, BFU-E were more evenly distributed between the three cell populations. Stem cell activity was measured by the long-term culture-initiating cell (LTC-IC) limiting dilution assay. The number of LTC-IC per reactor consistently increased with time in all cultures, resulting in a 7.5-fold (range, 3.4- to 9.8- fold) expansion. In summary, more than 3 billion cells, containing 12 million CFU-GM, were reproducibly generated from the equivalent of a 10 to 15 ml BM aspirate. These data indicate that small numbers of BM MNC can be readily expanded ex vivo in continuous perfusion cultures, and that such ex vivo expansion may have direct applications in clinical and experimental BM transplantation.
Comparison of colon adenoma detection rates using cap-assisted and Endocuff-assisted colonoscopy: a randomized controlled trial

Abstract Objectives and study aim Colonoscopy prevents colorectal cancer by removing adenomatous polyps, but missed adenomas lead to interval cancers. Different devices have been used to increase adenoma detection rates (ADR). Two such devices of interest are the transparent cap (Olympus) and Endocuff (ARC Medical). Our study aimed to compare differences in ADR between Endocuff-assisted colonoscopy (EAC), cap-assisted colonoscopy (CAC) and standard colonoscopy (SC). Patients and methods A sample size of 126 subjects was calculated to determine an effect size of 30 %. Patients undergoing screening or surveillance colonoscopy between March 2016 and January 2017 were randomized to SC, CAC or EAC groups. Three experienced endoscopists performed all colonoscopies. Patient demographics, procedure indication, Boston Bowel Prep Score (BBPS), withdrawal time, polyp size, location, histopathology, were analyzed. Results There was no difference in ADR (52 %, 40 % and 54 %) in the SC, CAC and EAC groups respectively (P = 0.4). Similar findings were also observed for proximal ADR (45 %, 35 %, and 50 %, P = 0.4) and SSA detection rate (16 %, 14 %, and 23 %, P = 0.5). EAC detected higher mean ADR per colonoscopy compared to CAC (1.70 vs 0.76, P = 0.01). However, there was no significant difference in mean ADR per positive colonoscopy (2.08, 1.63, and 2.59, P = 0.21). Conclusion In a randomized controlled trial comparing AC to CAC and SC, neither device conferred additional benefits in ADR among high detectors. When comparing each device, EAC may be better than CAC at detecting more total adenomas.
The Survey of Income and Program Participation Aapor Roundtable: Improving Income Measurement

The Census Bureau established the SIPP Methods Panel project to evaluate and redesign the core instrument for SIPP, a recurring, nationally representative, longitudinal survey of people and their socioeconomic characteristics. The objectives of the project are to improve response rates in SIPP, to reduce burden, and to improve data quality. It is a research project consisting of analysis of extant data as well as experimental research. The data analysis component includes examining patterns of nonresponse, examining reporting patterns across waves of interviewing, and analyzing patterns of income receipt. The program of experimental research consists of three phases, designed to allow for three iterations of testing and refining the Wave 1 core instrument and two iterations for Wave 2. Each experiment involves the selection of an independent sample of the population in six regional offices—half of which are to be randomly assigned to a control group, and half assigned to a treatment group. Each sample is designed to have 2000 interviewed cases, with the half in the control group receiving the SIPP instrument in the field at the time of the experiment and the other half in the treatment group receiving an experimental instrument. The AAPOR roundtable discussion presents findings from the first two field tests conducted in summer 2000 and summer and fall 2001 and uses that to promote dialogue on successful approaches to designing instruments for complex longitudinal surveys. Topics to address include approaches to reducing item nonresponse and income underreporting, methods of collecting earnings and their impact on response rates and data quality, nonresponse follow up techniques and their success, methods of improving interview efficiency and assessment of interviewer satisfaction, the success of new methods of assessing within household coverage, and a cognitive assessment of dependent interviewing techniques. Background The Survey of Income and Program Participation (SIPP) is a longitudinal survey conducted by the U.S. Census Bureau to provide data on the distribution of income, wealth, and poverty in the United States, and on the effects of federal and state programs on families and individuals. Currently, SIPP consists of nine waves, or rounds of interviewing, with each wave administered every four months to a nationally representative sample of the civilian noninstitutionalized population. Interviewing for each wave is distributed over four successive calendar months to create a stable production workload for field staff. It is primarily a person-based survey, administering a battery of questions to each person age 15 …
Comparative and Analysis Study for Malicious Executable by Using Various Classification Algorithms

: - There are a lot of applications regarding the data mining methods in detecting malwares. One of the most widely utilized data mining methods is the Classification method. In our research, we are presenting a data mining classification procedure through applying machine learning algorithms to detect malicious executable files, and this study will investigate the approach of classification in some algorithms such as (Support Vector Machine, Random Forest, KNN (k-Nearest Neighbors Classifier), and The Hoeffding Tree). In our classification process, we used some of well-known machine-learning algorithms by WEKA libraries, and then we train our dataset to detect malware. We made a comparative analysis between algorithms used and how they deal with the selected features based on the size of the data, to illustrate the performance efficiency. Where we got a high accuracy up to 98% with Random Forest. Moreover, this study is considered as a base for future studies regarding malware analysis through machine learning algorithms.
Geophysical studies relating to the tectonic structure, geothermal fields and geomorphological evolution of the Sperchios River Valley, Central Greece

An integrated geophysical investigation including resistivity, gravity and SP measurements is used to reveal the overall tectonic status of the Sperchios River Valley, Central Greece, as well as the sedimentation of the valley at various depths in view of the geothermal status. Deep Schlumberger soundings are interpreted by 2D models and then used to constrain the density values in the corresponding gravity profiles. The combined interpretation of resistivity and gravity measurements suggests that the valley consists of deep sediments mainly of clayey origin and the valley fill reaches two kilometers beneath the Delta. The depth of the bedrock (which has ophiolite or flysch and limestone underneath) is controlled by some buried faults mainly of E-W strike. Other faults of NNW-SSE strike create some sinkings and uplifts in the bedrock relief. The interpretation of geophysical data verifies blocky shaped bedrock. Such a fault system in the southern part of the valley is also related to geothermal surface manifestations. Faults in the flysch give rise to a deep passage for geothermal fluids which reach the surface through geothermal circulation zones in the sediments detected by the SP method. The deposition of the Sperchios River and its torrents, and the tectonic activity (sinkings and uplifts in the bedrock detected by the whole geophysical survey), mainly affect character of the sedimentation (shown by resistivity interpretation) and river routes.
Collaborative development of annotation guidelines with application to Universal Dependencies

We introduce an online linguistic annotation guideline development system that supports simple authoring, visualization of complex structured annotation, version control, and rich collaboration features. The system is presented in the context of a project aiming to develop universally applicable treebank annotation guidelines and apply them to a broad range of languages. The system is open source and available from http://spyysalo.github. io/annodoc/, and the Universal Dependencies documentation is available from http://universaldependencies.github. io/docs/.
ITEC-UNIKLU Ad-hoc Video Search Submission 2017

This paper describes our approach used for the fully automatic and manually assisted Ad-hoc Video Search (AVS) task for TRECVID 2017. We focus on the combination of diﬀerent convolutional neural network models and query optimization. Each of this model focus on a speciﬁc query part, which could be, e.g., location, objects, or the wide-ranging ImageNet classes. All classiﬁcation results are collected in diﬀerent combinations in Lucene indixes. For the manually assisted run we use a junk ﬁlter and diﬀerent query optimization methods.
Dendrimer-Based Drug Delivery Systems for Brain Targeting

Human neuroscience has made remarkable progress in understanding basic aspects of functional organization; it is a renowned fact that the blood–brain barrier (BBB) impedes the permeation and access of most drugs to central nervous system (CNS) and that many neurological diseases remain undertreated. Therefore, a number of nanocarriers have been designed over the past few decades to deliver drugs to the brain. Among these nanomaterials, dendrimers have procured an enormous attention from scholars because of their nanoscale uniform size, ease of multi-functionalization, and available internal cavities. As hyper-branched 3D macromolecules, dendrimers can be maneuvered to transport diverse therapeutic agents, incorporating small molecules, peptides, and genes; diminishing their cytotoxicity; and improving their efficacy. Herein, the present review will give exhaustive details of extensive researches in the field of dendrimer-based vehicles to deliver drugs through the BBB in a secure and effectual manner. It is also a souvenir in commemorating Donald A. Tomalia on his 80th birthday.
New responsibilities for aged kinases in B‐lymphomas

The knowledge accumulated over the last decade on B‐cell–derived non‐Hodgkin lymphoma (B‐NHL) pathogenesis has led to the identification of several molecular abnormalities, opening new perspectives in the design of novel therapies. Indeed, drugs targeting specific biochemical pathways critical for B‐NHL cell survival, proliferation, and fitness within the malignant microenvironment are now available to the clinician: the B‐cell receptor signaling inhibitors of BTK, PI3Kδ, ζ, γ, and SYK or the pro‐apoptotic BH3‐mimetics are clear examples of it. Moreover, it is emerging that malignant B‐cell growth is sustained not only by mutations in oncogenes/tumor suppressors but also by the “addiction” to nononcogene (ie, nonstructurally altered) molecules. In this regard, a consistent body of data has established that the Ser/Thr kinases CK1, CK2, and GSK3 are involved in malignant lymphocyte biology and act as pro‐survival and signaling‐boosting molecules, both in precursor and mature B‐cell tumors. Currently, an experimental and clinical groundwork is available, upon which to design CK1‐, CK2‐, and GSK3‐directed antilymphoma/leukemia therapies. In this review, we have examined the main features of CK1, CK2, and GSK3 kinases, summarized the data in B‐NHL supporting them as suitable therapeutic targets, and proposed a perspective on potential future research development.
Environmental Influences on Mammographic Breast Density in California: A Strategy to Reduce Breast Cancer Risk

State legislation in many U.S. states, including California, mandates informing women if they have dense breasts on screening mammography, meaning over half of their breast tissue is comprised of non-adipose tissue. Breast density is important to interpret screening sensitivity and is an established breast cancer risk factor. Environmental chemical exposures may play an important role in this, especially during key windows of susceptibility for breast development: in utero, during puberty, pregnancy, lactation, and the peri-menopause. There is a paucity of research, however, examining whether environmental chemical exposures are associated with mammographic breast density, and even less is known about environmental exposures during windows of susceptibility. Now, with clinical breast density scoring being reported routinely for mammograms, it is possible to find out, especially in California, where there are large study populations that can link environmental exposures during windows of susceptibility to breast density. Density scores are now available throughout the state through electronic medical records. We can link these with environmental chemical exposures via state-wide monitoring. Studying the effects of environmental exposure on breast density may provide valuable monitoring and etiologic data to inform strategies to reduce breast cancer risk.
The impact of miR‐183/182/96 gene regulation on the maturation, survival, and function of photoreceptor cells in the retina

MicroRNAs (MiRNAs) play important roles in posttranscriptional processes to regulate gene expression. MiRNAs control various biological processes, such as growth, development, and differentiation. The continuous physiological function of photoreceptors and retinal pigment epithelium requires precise regulation to maintain their homeostasis and function; hence, these cells are highly susceptible to premature death in retinal degenerative disorders. MiRNAs are essential for the retinal cell maturation and function; the miR‐183 cluster represents one of the most important regulatory factors for the photoreceptor cells. Various studies together with bioinformatics analyses have shown that many genes contributing to the differentiation pathway of photoreceptors are targets of the miR‐183 cluster, and the miR‐183 cluster dysregulation causes certain defects in the differentiation of the photoreceptors and other retinal neurons by influencing the expression of target genes. Misexpression of miR‐183 cluster in the human retinal epithelial cells leads to the reprogramming and transformation of these cells to neuron‐ and photoreceptor‐like cells, which are associated with the expression of neuron‐ and photoreceptor‐specific markers in human retinal pigment epitheliums cells. The knockout of this cluster causes the destruction of the outer segment of the photoreceptors, which subsequently causes the cells to exhibit severe susceptibility to light and eventually degenerate. Hundreds of target genes in this family are likely to affect the development and maintenance of the retina. Identifying the genes that are regulated by the miRNA‐183 cluster provides researchers with important insights into the complex development and regeneration mechanism of the retina and may offer a new way for maintaining and regenerating photoreceptor cells in neurodegenerative diseases.
A nanoscale view of amyloid photodynamic damage.

A combination of time-resolved optical spectroscopy and nanoscale imaging has been used to study the complex binding to amyloids of a photocatalyst that selectively photo-oxygenates pathogenic aggregates, as well as the consequences of its irradiation. Correlative atomic force microscopy (AFM) and fluorescence microscopy reveals topography-dependent binding of the dye to model β-lactoglobulin fibers, which may also explain the observed difference in their response to photodegradation. We provide direct evidence of the photosensitization of singlet oxygen by the photocatalyst bound to amyloid fibers by direct detection of its NIR phosphorescence. The effect of singlet oxygen at the molecular level brings about nanoscale morphological changes that can be observed with AFM at the single-fiber level. We also find differential response of two α-synuclein mutants to photodamage, which can be rationalized by the presence of amino acids susceptible to photo-oxygenation. Overall, our results help to unravel some of the complexity associated to highly heterogeneous amyloid populations, and contribute to the development of improved phototherapeutic strategies for amyloid-related disorders.
In vitro metabolism of sunscreen compounds by liquid chromatography-high resolution tandem mass spectrometry.

RATIONALE Exposure to UV light can induce adverse effects on human health, such as photo-aging, immunosuppression, and cancer. Sunscreens are used to prevent the absorption of UV rays, but certain UV-filtering compounds have been shown to disrupt endocrine systems or act as carcinogens. To assess the effects of the exposure to such compounds, it is important to study the pathways in which they are biotransformed in the body. METHODS Liquid chromatography coupled to high-resolution tandem mass spectrometry (LC/HRMS/MS) was employed to evaluate the oxidative metabolism and, specifically, the formation of reactive metabolites of six active ingredients commonly used in sunscreen formulations: oxybenzone, avobenzone, homosalate, octisalate, octocrylene, and octinoxate. In vitro incubations were performed with human and rat liver microsomes in the presence of β-nicotinamide adenine dinucleotide phosphate and glutathione. An LC/HRMS/MS method was developed to identify metabolites employing a biphenyl reverse-phase column for separating parent molecules, metabolites, and glutathione adducts. RESULTS Each tested compound resulted in the formation of several metabolites, including at least one GSH adduct. Compounds containing ester groups were hydrolyzed, and some metabolites of the free acid forms were also detected. High-resolution MS/MS data was crucial for the structural elucidation of metabolites and GSH adducts. Fragmentation pathways were proposed for all parent compounds, as well as each described metabolite and adduct. CONCLUSIONS The results of this study will help better understand the metabolism and detoxification pathways of these xenobiotics.
In-Depth Analysis of Unmodulated Visible Light Positioning Using the Iterated Extended Kalman Filter

Indoor positioning with visible light has become increasingly important in recent years. Usually, light sources are modulated at high speeds in order to wirelessly transmit data from the fixtures to a receiver. The accuracy of such systems can range from a few decimeters to a few centimeters. However, additional modulation hardware is required for every light source, thereby increasing cost and system complexity. This paper investigates the use of unmodulated light for indoor positioning. Contrary to previous work, a Kalman filter is used instead of a particle filter to decrease the computational load. As a result, the update rate of position estimation can be higher. Additionally, more resources could be made available for other tasks (e.g., path planning for autonomous robots). We evaluated the performance of our proposed approach through simulations and experiments. The accuracy depends on a number of parameters, but is generally lower than 0.5 m. Moreover, temporary occlusion of the receiver can be compensated in most cases.
Dormancy cycling: translation‐related transcripts are the main difference between dormant and non‐dormant seeds in the field

Summary Primary seed dormancy is a mechanism that orchestrates the timing of seed germination in order to prevent out‐of‐season germination. Secondary dormancy can be induced in imbibed seeds when they encounter prolonged unfavourable conditions. Secondary dormancy is not induced during dry storage, and therefore the mechanisms underlying this process have remained largely unexplored. Here, a 2‐year seed burial experiment in which dormancy cycling was studied at the physiological and transcriptional level is presented. For these analyses six different Arabidopsis thaliana genotypes were used: Landsberg erecta (Ler) and the dormancy associated DELAY OF GERMINATION (DOG) near‐isogenic lines 1, 2, 3, 6 and 22 (NILDOG1, 2, 3, 6 and 22). The germination potential of seeds exhumed from the field showed that these seeds go through dormancy cycling and that the dynamics of this cycling is genotype dependent. RNA‐seq analysis revealed large transcriptional changes during dormancy cycling, especially at the time points preceding shifts in dormancy status. Dormancy cycling is driven by soil temperature and the endosperm is important in the perception of the environment. Genes that are upregulated in the low‐ to non‐dormant stages are enriched for genes involved in translation, indicating that the non‐dormant seeds are prepared for rapid seed germination.