Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of variable sample biomass on comparative metagenomics.

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys.
Cryogenic‐temperature electron microscopy direct imaging of carbon nanotubes and graphene solutions in superacids

Cryogenic electron microscopy (cryo‐EM) is a powerful tool for imaging liquid and semiliquid systems. While cryogenic transmission electron microscopy (cryo‐TEM) is a standard technique in many fields, cryogenic scanning electron microscopy (cryo‐SEM) is still not that widely used and is far less developed. The vast majority of systems under investigation by cryo‐EM involve either water or organic components. In this paper, we introduce the use of novel cryo‐TEM and cryo‐SEM specimen preparation and imaging methodologies, suitable for highly acidic and very reactive systems. Both preserve the native nanostructure in the system, while not harming the expensive equipment or the user. We present examples of direct imaging of single‐walled, multiwalled carbon nanotubes and graphene, dissolved in chlorosulfonic acid and oleum. Moreover, we demonstrate the ability of these new cryo‐TEM and cryo‐SEM methodologies to follow phase transitions in carbon nanotube (CNT)/superacid systems, starting from dilute solutions up to the concentrated nematic liquid‐crystalline CNT phases, used as the ‘dope’ for all‐carbon‐fibre spinning. Originally developed for direct imaging of CNTs and graphene dissolution and self‐assembly in superacids, these methodologies can be implemented for a variety of highly acidic systems, paving a way for a new field of nonaqueous cryogenic electron microscopy.
The Ras effector RASSF2 is a novel tumor-suppressor gene in human colorectal cancer.

BACKGROUND & AIMS Activation of Ras signaling is a hallmark of colorectal cancer (CRC), but the roles of negative regulators of Ras are not fully understood. Our aim was to address that question by surveying genetic and epigenetic alterations of Ras-Ras effector genes in CRC cells. METHODS The expression and methylation status of 6 RASSF family genes were examined using RT-PCR and bisulfite PCR in CRC cell lines and in primary CRCs and colorectal adenomas. Colony formation assays and flow cytometry were used to assess the tumor suppressor activities of RASSF1 and RASSF2. Immunofluorescence microscopy was used to determine the effect of altered RASSF2 expression on cell morphology. Mutations of K- ras , BRAF, and p53 were identified using single-strand conformation analysis and direct sequencing. RESULTS Aberrant methylation and histone deacetylation of RASSF2 was associated with the gene's silencing in CRC. The activities of RASSF2, which were distinct from those of RASSF1, included induction of morphologic changes and apoptosis; moreover, its ability to prevent cell transformation suggests that RASSF2 acts as a tumor suppressor in CRC. Primary CRCs that showed K- ras /BRAF mutations also frequently showed RASSF2 methylation, and inactivation of RASSF2 enhanced K- ras -induced oncogenic transformation. RASSF2 methylation was also frequently identified in colorectal adenomas. CONCLUSIONS RASSF2 is a novel tumor suppressor gene that regulates Ras signaling and plays a pivotal role in the early stages of colorectal tumorigenesis.
How Sourcing of Interdependent Components Affects Quality in Automotive Supply Chains

In the automotive industry, many firms source key components from different suppliers, even though the components may function interdependently. In this study, we investigate how component level interdependence impacts quality performance and analyze how various operational factors moderate this relation. We synthesize information from several case studies to model the quality challenges faced by an automotive firm. For several sub‐assemblies that go into its products, the firm sourced key components from two different suppliers. The sub‐assemblies would fail whenever a component fails, but due to interdependent operations, failure of one component could cause the failure of the other. The firm found it challenging to improve the suppliers' quality performance as it was difficult to trace the failures to specific components. Our analysis reveals that – (i) the impact of interdependence is governed by the supply chain structure: reducing the interdependence between components improves quality when suppliers provide the components, but reducing interdependence worsens quality when the firm manufactures the entire sub‐assembly; and (ii) the relation between interdependence and quality performance is moderated by factors such as penalties, production costs, and interdependence costs. Additionally, we find that quality performance is lower when the firm outsources the components than when the firm manufactures the entire sub‐assembly. We identify coordinating mechanisms that leverage incentives and penalties to bridge the quality performance gap.
Comparison of Point-of-Care HbA1c Test versus Standardized Laboratory Testing

BACKGROUND: Glycosylated hemoglobin (HbA1c) evaluation is an accepted standard of care for assessing diabetes control. Point-of-care HbA1c monitors are relatively new, and there are few published data on their accuracy. OBJECTIVE: To compare a point-of-care HbA1c monitor with standardized laboratory testing. METHODS: Twenty-three patients who had type 1 or 2 diabetes were identified from our pharmacy-run diabetes clinic at a primary care clinic as needing HbA1c evaluation based on the American Diabetes Association guidelines. All patients with diabetes who attended our clinic were invited to participate in the study. Patients were required to obtain both a standardized laboratory HbA1c evaluation and a point-of-care A1c Now value within a week of each other. An analysis evaluating both clinical and statistical significance was completed at the end of the study. RESULTS: The A1c Now monitor showed good correlation (r = 0.758) to the standardized laboratory test. We found that the most accurate A1c Now values were within a range of 6–8%. One patient's value would have resulted in a different clinical decision if the decision were based on the A1c Now value. CONCLUSIONS: It appears that A1c Now may provide adequate accuracy and be useful for some patients. The monitor would be most beneficial for patients who cannot obtain standardized laboratory values secondary to either financial or transportation constraints. However, the decision to make adjustments in therapy should not be based solely on the A1c Now point-of-care result.
Test of a Robust ZMP Based Pattern Generator with a 12-Internal-DoF Biped Robot Model

In this contribution one pattern generator from the literature is tested with a multibody model of a 12-internal-DoF biped robot: a recently proposed generator based on sliding modes, which can be seen as a robustificated version of a classical algorithm. As proposed in the literature, the feedback of the multibody tracking error improve the performance of the multibody ZMP, which is now tested for this sliding-mode-based generator. A bounded disturbance in the multibody model was considered also to test the robustness of the techinque. Tunning complexity issues of the robust generator are also discussed.
Effect of Robo1 on retinal pigment epithelial cells and experimental proliferative vitreoretinopathy.

PURPOSE The Roundabout (Robo) family of proteins is related to the transmembrane receptors and plays a major role in neurogenesis. However, the role of the Robo proteins in proliferative retinopathy has not yet been defined. This study was conducted to determine whether Robo1 is expressed in the retina of patients with proliferative retinal disease and whether it has a pathobiological role in the disease. METHODS Immunohistochemistry was used to determine the presence and distribution of Robo1 in the pathologic membranes in proliferative retinopathy. Small interfering (si)RNA technology was used to knockdown Robo1 expression and to study its effects on retinal pigment epithelial (RPE) cells in vitro. The impact on PVR development of blocking Robo1 expression was determined by applying specific siRNA in a PVR rabbit model. The prevalences of PVR and retinal detachment were determined by indirect ophthalmoscope on days 1, 3, 7, 14, 21, and 28 after the injection of RPE cells into the vitreous. RESULTS Immunohistochemistry showed that Robo1 expression was detected in GFAP-labeled glial cells and cytokeratin-labeled RPE cells in proliferative membranes. Robo1 expression was also detected in CD31-labeled vascular endothelial cells. Knockdown of Robo1 expression not only reduced human RPE cell proliferation in vitro but also effectively suppressed the development of PVR in a rabbit model. CONCLUSIONS Robo1 is present in the extracellular matrix of proliferative membranes and may be derived from dedifferentiated RPE cells. Silencing the expression of Robo1 in RPE cells inhibited cell proliferation and suppressed the development of PVR in an animal model, indicating a potential therapeutic usefulness in treating PVR.
Principles of smile design

An organized and systematic approach is required to evaluate, diagnose and resolve esthetic problems predictably. It is of prime importance that the final result is not dependent only on the looks alone. Our ultimate goal as clinicians is to achieve pleasing composition in the smile by creating an arrangement of various esthetic elements. This article reviews the various principles that govern the art of smile designing. The literature search was done using PubMed search and Medline. This article will provide a basic knowledge to the reader to bring out a functional stable smile.
“Going Beyond the Call of Doula”: A Grounded Theory Analysis of the Diverse Roles Community-Based Doulas Play in the Lives of Pregnant and Parenting Adolescent Mothers

This article presents some of the most salient qualitative results from a larger program evaluation of pregnant and parenting adolescents who participated in a community-based doula program. Using grounded theory analysis, seven problem-solving strategies emerged that doulas apply in helping pregnant and parenting adolescents navigate multiple social and health settings that often serve as barriers to positive maternal- and child-health outcomes. The ethnographic findings of this study suggest that the doulas provide valuable assistance to pregnant and parenting adolescents by addressing social-psychological issues and socio-economic disparities. “Diverse role-taking” results in doulas helping pregnant adolescents navigate more successfully through fragmented social and health service systems that are less supportive of low-income adolescents, who are often perceived to be draining scarce resources. The findings have implications for the roles of community-based doulas assigned to low-income adolescents of color seeking to overcome obstacles and attain better educational and economic opportunities.
Integrated science and art education for creative climate change communication

An interdisciplinary field trip to a remote marine lab joined graduate students from fine arts and natural resource science departments to think creatively about the topic of climate change and science communication. We followed a learning cycle framework to allow the students to explore marine ecosystems and participate in scientific lectures, group discussions, and an artist-led project making abstract collages representing climate change processes. Students subsequently worked in small groups to develop environmental communication material for public visitors. We assessed the learning activity and the communication product using pre- and post-field trip participant surveys, focus group discussions, and critiques by art and communication experts of the products. Significant changes in knowledge about climate change occurred in program participants. Incorporating artists and the arts into this activity helped engage multiple senses and emphasized social interaction, as well as providing support to participants to think creatively. The production of art helped to encourage peer learning and normalize the different views among participants in communicating about climate change impacts. Students created effective communication products based on external reviews. Disciplinary differences in cultures, language, and standards challenged participating faculty, yet unanticipated outcomes such as potentially transformative learning and improved teacher evaluations resulted.
Relationship between various maternal conditions and lactic acid dehydrogenase activity in umbilical cord blood at birth

Abstract Background: Lactic acid dehydrogenase (LDH) is a valuable marker for some of the most important diseases in newborns and the plasma LDH activity in newborns correlates well with conditions such as asphyxia. If LDH should be considered as a useful tool also in obstetric care, key factors associated with maternal health before and during pregnancy which could affect umbilical cord LDH activity need to be known. The aims of this study were to explore relationships between selected maternal conditions and arterial lactic acid dehydrogenase activity (aLDH) in umbilical cord blood at delivery. Methods: A prospective observational study was conducted at Sodersjukhuset, Stockholm, Sweden. Included in the study were 1247 deliveries, and cord blood samples from each were analyzed for aLDH. Background, delivery and neonatal data were collected from the medical records. Results: Higher median values of aLDH were found (P=0.001) among women with chronic disorders not related to pregnancy but there was no increased frequency of high aLDH levels (>612 μ/L, P=0.30). No difference in aLDH was identified between infants born to women with pregnancy-related disorders compared with healthy women, neither in median values, nor in high values (>612 μ/L, P=0.95). Conclusion: Newborn infants born to women with non-pregnancy-related chronic disorders had a somewhat higher median value of aLDH in cord blood at delivery. The influence of common maternal conditions and diseases on umbilical cord arterial LDH levels is small compared to the increase reported in fetal distress and several other critical conditions in the newborn.
Successful Oocyte Cryopreservation in Reproductive-Aged Cancer Survivors

OBJECTIVE: To demonstrate that oocyte cryopreservation is a feasible reproductive option for patients with cancer of childbearing age who require gonadotoxic therapies. METHODS: This study is a university-based retrospective review of reproductive-aged cancer patient treatment cycles that included ovarian stimulation, transvaginal oocyte retrieval, oocyte cryopreservation, and, in some cases, subsequent oocyte thaw, in vitro fertilization, and embryo transfer. Outcome measures included ovarian stimulation response, number of oocytes retrieved, cryopreserved, and thawed, and pregnancy data. RESULTS: From 2005 to 2014, 176 reproductive-aged patients with cancer (median age 31 years, interquartile range 24–36) completed 182 oocyte cryopreservation cycles. Median time between consult request and oocyte retrieval was 12 days (interquartile range 10–14). Median peak stimulation estradiol was 1,446 pg/mL (interquartile range 730–2,687); 15 (interquartile range 9–23) oocytes were retrieved and 10 (interquartile range 5–18) metaphase II oocytes were cryopreserved per cycle. Ten patients (11 cycles) have returned to attempt pregnancy with their cryopreserved oocytes. Among thawed oocytes, the cryopreservation survival rate was 86% (confidence interval [CI] 78–94%). Nine of 11 thaw cycles resulted in embryos suitable for transfer. The embryo implantation rate was 27% (CI 8–46%) and the live birth rate was 44% (CI 12–77%) per embryo transfer. Chance for live birth with embryos created from cryopreserved oocytes was similar between the patients with cancer in this study and noncancer patients who underwent the same treatment at our center (44% [CI 12–77%] compared with 33% [CI 22–44%] per embryo transfer). CONCLUSION: Oocyte cryopreservation is now a feasible fertility preservation option for reproductive-aged patients with cancer who require gonadotoxic therapies.
Menstruation in Girls and Adolescents: Using the Menstrual Cycle as a Vital Sign

Young patients and their parents often are unsure about what represents normal menstrual patterns, and clinicians also may be unsure about normal ranges for menstrual cycle length and amount and duration of ﬂow through adolescence. It is important to be able to educate young patients and their parents regarding what to expect of a ﬁrst period and about the range for normal cycle length of subsequent menses. It is equally important for clinicians to have an understanding of bleeding patterns in girls and adolescents, the ability to differentiate between normal and abnormal menstruation, and the skill to know how to evaluate young patients’ conditions appropriately. Using the menstrual cycle as an additional vital sign adds a powerful tool to the assessment of normal development and the exclusion of pathological conditions.
Determinants of Islamic banking adoption in Ghana

Purpose This study aims to examine factors affecting the adoption of Islamic banking (IB), which is an innovative and emerging form of banking, in a non-Islamic Sub-Saharan African (SSA) country. Design/methodology/approach It used primary data collected from a cross-section of 975 respondents using self-administered structured questionnaire. Empirical data were analysed using SPSS version 16 and partial least squares structural equation modelling (PLS-SEM) for Muslim and non-Muslim groups. Findings Consumer attitude, readiness to comply with Sharia law, knowledge, perceived innovativeness and perceived benefits were critical determinants of bank customers’ intention to adopt IB in both Muslim and non-Muslim sub-groups. The least influential factors were perceived religion effect (PRE) and perceived threat of violence (PTV). PTV was not a significant factor to non-Muslims, but it was a significantly negative factor to Muslims’ intentions to adopt IB. PRE has a positive influence on Muslims’ intention to adopt IB, but it has a negative effective on non-Muslims’ adoption intentions. Research limitations/implications This study is limited to only bank customers in Ghana. Moreover, service quality factors were not included in the research model because IB is yet to be given full-fledged operational license in Ghana. Future research should extend the study to other emerging countries to improve the generalizability of the findings. Practical implications Policymakers are encouraged to develop stakeholder-oriented strategies to promote effective consumer education in IB. Also, IB institution should endeavour to develop innovative financial products that are Sharia-compliant and economically beneficial to individual and business needs of bank customers. Moreover, policymakers and management of IB institutions should ensure effect governance structures to guide IB operations. Originality/value This study provides initial structural equation modelling of determinants of IB adoption in emerging countries and provides empirical evidence on the spread of IB in non-Islamic SSA, which is an under-researched area. It is the first study to empirically report on the influence of PTV, readiness to compliance Sharia law and perceived innovativeness of IB on intentions to adopt IB in non-Islamic SSA context.
CTCF Is Essential for Up‐Regulating Expression from the Amyloid Precursor Protein Promoter During Differentiation of Primary Hippocampal Neurons

Abstract : The transcriptional mechanism underlying amyloid precursor protein (APP) regulation in primary neurons during development was investigated. We observed an approximately threefold elevation of APP mRNA levels in differentiating rat hippocampal neurons between day 1 and day 7 in culture and in rat brain hippocampi between embryonic day 18 and postnatal day 3. When an APP promoter construct extending to position ‐2,832 upstream from the main transcriptional start site was transfected into primary rat hippocampal neurons, promoter activity increased from day 1 until reaching a maximum on day 7 in culture. This increase in APP promoter activity was correlated more closely with the time course of expression of the synaptic vesicle protein synaptophysin, an indicator of synaptogenesis, than with neurofilament accumulation, an indicator of neuritogenesis. Transfection of 5′ APP promoter deletions and internal block mutations indicated that the CTCF binding domain designated APBβ was the primary contributor to the increase in APP promoter activity. Furthermore, the binding of transcription factor CTCF to the APBβ element increased approximately fivefold between day 1 and day 7, whereas the binding of USF to the APBα sequence increased only twofold. These results suggest that CTCF is pivotal for the up‐regulation of APP expression during synaptogenesis in primary neurons.
Effect of Arousal and Retention Delay on Memory: A Meta-Analysis

Two meta-analyses were conducted to examine the magnitude of the interaction between arousal and retention delay on various types of memory, e.g., verbal, visual, etc., as initially reported by Kleinsmith and Kaplan in 1963 and 1964. Results of the first meta-analysis (29 studies, N = 2,637) indicated that the interaction was robust (d = .779), with low arousal leading to better immediate memory than high arousal, whereas high arousal led to better delayed memory than low arousal. Incorporating additional studies, a subsequent meta-analysis (48 studies, N = 3,143) on the effect of arousal on memory, taking retention delay as a moderator, provided further support. At a 2-min. delay, low arousal led to better immediate memory than high arousal (d = –.459). This difference decreased at a 20-min. delay (d = .106), when directions of high and low arousal effects on memory appeared to reverse. At longer delays than 20 min., high arousal led to better delayed memory than low arousal (ds = .753, .219, and .472, for delays of 45-min., 1-day, and more than 1-day, respectively).
Evolution of CXCR4-Using Human Immunodeficiency Virus Type 1 SF162 Is Associated with Two Unique Envelope Mutations

ABSTRACT CCR5-using human immunodeficiency virus type 1 (HIV-1) isolates typically gain CXCR4 use via multiple mutations in V3 and often V1/V2 regions of envelope, and patterns of mutations are distinct for each isolate. Here, we report that multiple CXCR4-using variants of a parental CCR5-using HIV-1 isolate, SF162, obtained by either target cell selection or CCR5 inhibition have a common mutation pattern characterized by the same two V3 mutations and that these mutations preexisted in some of the SF162 stocks. These results imply that SF162 has a single pathway for acquiring CXCR4 use and that prolonged culture is sufficient to select for R5X4 variants.