Miracle-dz/UniFAR-FTUs huggingface dataset:
Conditionally Rare Taxa Contribute but Do Not Account for Changes in Soil Prokaryotic Community Structure

The rare biosphere is predicted to aid in maintaining functional redundancy as well as contributing to community turnover across many environments. Recent developments have partially confirmed these hypotheses, while also giving new insights into dormancy and activity among rare communities. However, less attention has been paid to the rare biosphere in soils. This study provides insight into the rare biosphere’s contribution to soil microbial diversity through the study of 781 soil samples representing 24 edaphically diverse sites. Results show that Bray–Curtis dissimilarity for time-sensitive conditionally rare taxa (CRT) does not correlate with whole community dissimilarity, while dissimilarity for space-sensitive CRT only weakly correlate with whole community dissimilarity. This adds to current understanding of spatiotemporal filtering of rare taxa, showing that CRT do not account for community variance across tested soils, but are under the same selective pressure as the whole community.
Estimating city-level travel patterns using street imagery: A case study of using Google Street View in Britain

Background Street imagery is a promising and growing big data source providing current and historical images in more than 100 countries. Studies have reported using this data to audit road infrastructure and other built environment features. Here we explore a novel application, using Google Street View (GSV) to predict travel patterns at the city level. Methods We sampled 34 cities in Great Britain. In each city, we accessed 2000 GSV images from 1000 random locations. We selected archived images from time periods overlapping with the 2011 Census and the 2011–2013 Active People Survey (APS). We manually annotated the images into seven categories of road users. We developed regression models with the counts of images of road users as predictors. The outcomes included Census-reported commute shares of four modes (combined walking plus public transport, cycling, motorcycle, and car), as well as APS-reported past-month participation in walking and cycling. Results We found high correlations between GSV counts of cyclists (‘GSV-cyclists’) and cycle commute mode share (r = 0.92)/past-month cycling (r = 0.90). Likewise, GSV-pedestrians was moderately correlated with past-month walking for transport (r = 0.46), GSV-motorcycles was moderately correlated with commute share of motorcycles (r = 0.44), and GSV-buses was highly correlated with commute share of walking plus public transport (r = 0.81). GSV-car was not correlated with car commute mode share (r = –0.12). However, in multivariable regression models, all outcomes were predicted well, except past-month walking. The prediction performance was measured using cross-validation analyses. GSV-buses and GSV-cyclists are the strongest predictors for most outcomes. Conclusions GSV images are a promising new big data source to predict urban mobility patterns. Predictive power was the greatest for those modes that varied the most (cycle and bus). With its ability to identify mode of travel and capture street activity often excluded in routinely carried out surveys, GSV has the potential to be complementary to new and traditional data. With half the world’s population covered by street imagery, and with up to 10 years historical data available in GSV, further testing across multiple settings is warranted both for cross-sectional and longitudinal assessments.
Characterization of the Promoter Region of the Human c‐kit Proto‐oncogene

The c‐kit proto‐oncogene encodes a tyrosine kinase receptor for stem cell factor and plays a critical role in the growth and differentiation of various types of cells including hematopoietic stem cells. To investigate the mechanisms of its transcriptional regulation, we isolated the 5’flanking region of the human c‐kit gene and characterized its promoter activity in hematopoietic cells. Nucleotide sequence analysis revealed that the 1.2 kb 5’flanking region lacked a typical “TATA box,” but had a relatively high G + C content and four potential Sp1‐binding sites. Putative binding sites for AP‐2, basic helix‐loop‐helix proteins, Ets‐domain proteins, Myb and GATA‐1 were also found. Primer extension and S1 nuclease protection analyses of hematopoietic cells indicated that the major transcription start sites are 62 bp and 58 bp upstream of the translation start site. Essentially the same start sites were detected in non‐hematopoietic cells such as small cell lung carcinoma and glioblastoma: this single promoter in c‐kit is different from the multiple promoter system of c‐fms, a c‐kit‐related gene, in which at least two promoters are differently used in hematopoietic and non‐hematopoietic cells. An analysis of the c‐kit 5’flanking region using the bacterial chloramphenicol acetyltransferase gene (CAT assay) in human erythroleukemia HEL cells, which express the endogenous c‐kit mRNA at high levels, showed that a region from ‐180 to ‐22 is important for the expression of the c‐kit gene. In addition, a negative regulatory element(s) is suggested to be involved in the regulation of the c‐kit gene expression in mammals.
Pixantrone-rituximab versus gemcitabine-rituximab in relapsed/refractory aggressive non-Hodgkin lymphoma.

UNLABELLED We describe the rationale and design of the ongoing randomized, active-controlled, multicenter, Phase III study evaluating the efficacy of pixantrone and rituximab versus gemcitabine and rituximab in patients with diffuse large B-cell lymphoma or follicular grade 3 lymphoma, who are ineligible for high-dose chemotherapy and stem cell transplantation, and who failed front-line regimens containing rituximab. The administration schedule is pixantrone 50 mg/m(2) intravenously (iv.) or gemcitabine 1000 mg/m(2) iv. on days 1, 8 and 15, combined with rituximab 375 mg/m(2) iv. on day 1, up to six cycles. Pixantrone has a conditional European marketing approval for monotherapy in adults with multiple relapsed or refractory aggressive B-cell non-Hodgkin lymphoma. Our trial explores the efficacy of combining pixantrone with rituximab and completes postauthorization measures. TRIAL REGISTRATION NUMBER NCT01321541.
Honey clinically stimulates granulation and epithelialization in chronic wounds: a report of two cases

Various studies have been widely reintroduced honey as a wound dressing in chronic wound treatment. However, its utilization in Indonesia is still very limited. This study reported the effect of honey in stimulating the epithelialization and granulation on chronic wound treatment in our center. Two chronic wound cases, diabetic foot ulcer patient and gangrenous extravasation due to sodium bicarbonate, were daily treated with honey applications. After six-week evaluation, clinically the tissue granulation and epithelization were seen at the edge of the observed wounds and decreased the wound size significantly with no reported side effects. Honey clinically stimulates the epithelialization and granulation on chronic wound treatment.
Lung volumes identify an at-risk group in persons with prolonged secondhand tobacco smoke exposure but without overt airflow obstruction

Introduction Exposure to secondhand smoke (SHS) is associated with occult obstructive lung disease as evident by abnormal airflow indices representing small airway disease despite having preserved spirometry (normal forced expiratory volume in 1 s-to-forced vital capacity ratio, FEV1/FVC). The significance of lung volumes that reflect air trapping in the presence of preserved spirometry is unclear. Methods To investigate whether lung volumes representing air trapping could determine susceptibility to respiratory morbidity in people with SHS exposure but without spirometric chronic obstructive pulmonary disease, we examined a cohort of 256 subjects with prolonged occupational SHS exposure and preserved spirometry. We elicited symptom prevalence by structured questionnaires, examined functional capacity (maximum oxygen uptake, VO2max) by exercise testing, and estimated associations of those outcomes with air trapping (plethysmography-measured residual volume-to-total lung capacity ratio, RV/TLC), and progressive air trapping with exertion (increase in fraction of tidal breathing that is flow limited on expiration during exercise (per cent of expiratory flow limitation, %EFL)). Results RV/TLC was within the predicted normal limits, but was highly variable spanning 22%±13% and 16%±8% across the increments of FEV1/FVC and FEV1, respectively. Respiratory complaints were prevalent (50.4%) with the most common symptom being ≥2 episodes of cough per year (44.5%). Higher RV/TLC was associated with higher OR of reporting respiratory symptoms (n=256; r2=0.03; p=0.011) and lower VO2max (n=179; r2=0.47; p=0.013), and %EFL was negatively associated with VO2max (n=32; r2=0.40; p=0.017). Conclusions In those at risk for obstruction due to SHS exposure but with preserved spirometry, higher RV/TLC identifies a subgroup with increased respiratory symptoms and lower exercise capacity.
Oxidative stress as a cost of reproduction: Beyond the simplistic trade‐off model

The idea that oxidative stress may underpin life history trade‐offs has become extremely popular. However, experimental support for the concept has proved equivocal. It has recently been suggested that this might be because of flaws in the design of existing studies. Here, we explore the background to the oxidative stress hypothesis and highlight some of the complexities in testing it. We conclude that the approach recently suggested to be least useful in this context (comparing reproducing to non‐reproducing animals) may in fact be the most powerful. Moreover, suggested alternative approaches of limiting food supply or manipulating litter sizes have many complexities and problems. We suggest some useful alternative approaches that have not been previously advocated, particularly the study of individuals reproducing at greater parity later in life. Finally, the measures of oxidative stress and tissues that are analysed influence the experimental outcome. This suggests our conceptual model of the trade‐off is currently too simplistic, and that studies based on single or limited numbers of assays, or restricted to single tissues, whether they support or refute the theory, should be interpreted with great caution.
Biochemical Characterization of α‐Fetoprotein and Other Serum Proteins Produced by a Uterine Endometrial Adenocarcinoma

A high serum α‐fetoprotein (AFP) level was found in a patient with endometrial adenocarcinoma of the uterus, which appeared to be hepatoid on histological examination. The AFP of this unusual patient was purified hy immunoaffinity chromatography and characterized. The electrophoretic profiles on sodium dodecyl sulfate‐polyacrylamide gel electrophoresis both before and after glycopeptidase F treatment were indistinguishable from those of a hepatoma AFP. This indicates that the patient's AFP was also composed of a single polypeptide chain of Mr 67,000 and an N‐linked sugar chain of Mr 3,000. Amino acid sequence analyses of this AFP, and of AFP from hepatoma and umbilical cord serum indicated that the N‐terminal sequences were essentially the same. The sequence, Arg‐Thr‐Leu‐His‐Arg‐Asn‐Glu‐Tyr‐Gly‐Ile, was slightly different from previous reports, but matched that deduced from the cDNA sequence. AFP isoforms due to microheterogeneity of the sugar chain were analyzed by lectin affinity electrophoresis using a series of lectins. The AFP isoform profiles were distinct from those of proteins derived from cord serum, hepatoma, yolk sac tumor and gastric cancer. The reverse‐transcription of RNA from the tumor tissue followed by a polymerase chain reaction using primers with AFP‐specific sequences gave a product of the size and nucleotide sequence expected for AFP. mRNAs possessing the requisite sequences for albumin and transferrin syntheses were also detected in the tumor. The expression of these hepatocyte‐specific proteins supported the hepatoid nature of this tumor.
A longitudinal study of very young children's vowel production.

PURPOSE Ecologically realistic, spontaneous, adult-directed, longitudinal speech data of young children were described by acoustic analyses. METHOD The first 2 formant frequencies of vowels produced by 6 children from different American English dialect regions were analyzed from ages 18 to 48 months. The vowels were from largely conversational contexts and were classified according to dictionary pronunciation. RESULTS Within-subject formant frequency variability remained relatively constant for the span of ages studied. It was often difficult to detect overall decreases in the first 2 formant frequencies between ages 30 and 48 months. A study of the movement of the corner vowels with respect to the vowel centroid showed that the shape of the vowel space remained qualitatively constant from 30 through 48 months. CONCLUSIONS The shape of the vowel space is established early in life. Some aspects of regional dialect were observed in some of the subjects at 42 months of age. The present study adds to the existing data on the development of vowel spaces by describing ecologically realistic speech.
Hidden Reaction Norms, Cryptic Genetic Variation, and Evolvability

There is reason to suspect that hidden reaction norms (variation that is phenotypically expressed only after changes in internal or external environmental conditions) may store an evolutionarily significant pool of cryptic genetic variation upon which selection may act. I review mechanisms that may hide variation and the processes that can release this variation. I discuss the potential significance of cryptic genetic variation and elaborate on an example where the release of such variation initiated the evolution of the genetic architecture of multicellular organisms.
Autonomous Robotic Pick-and-Place of Microobjects

This paper presents a robotic system that is capable of both picking up and releasing microobjects with high accuracy, reliability, and speed. Due to force-scaling laws, large adhesion forces at the microscale make rapid, accurate release of microobjects a long-standing challenge in micromanipulation, thus representing a hurdle toward automated robotic pick-and-place of micrometer-sized objects. The system employs a novel microelectromechanical systems (MEMS) microgripper with a controllable plunging structure to impact a microobject that gains sufficient momentum to overcome adhesion forces. The performance was experimentally quantified through the manipulation of 7.5-10.9 ¿m borosilicate glass spheres in an ambient environment. Experimental results demonstrate that the system, for the first time, achieves a 100% success rate in release (which is based on 700 trials) and a release accuracy of 0.45 ± 0.24 ¿m. High-speed, automated microrobotic pick-and-place was realized by visually recognizing the microgripper and microspheres, by visually detecting the contact of the microgripper with the substrate, and by vision-based control. Example patterns were constructed through automated microrobotic pick-and-place of microspheres, achieving a speed of 6 s/sphere, which is an order of magnitude faster than the highest speed that has been reported in the literature.
Polybrominated Diphenyl Ether Exposure and Thyroid Function Tests in North American Adults

Background: Polybrominated diphenyl ethers (PBDEs) are flame-retardant chemicals that are added to many consumer products. Multiple animal studies have shown PBDEs to be thyroid hormone (TH) disruptors. Epidemiologic evidence of PBDE exposure associated with TH disruption has been inconclusive. Objectives: We used repeated measures to estimate associations between serum PBDE concentrations and THs in a North American adult cohort. Methods: From 2010 to 2011, we collected ≤ 3 serum samples at approximately 6-month intervals from 52 healthy adult office workers from Boston, Massachusetts, for analysis of PBDE congeners and THs. Results: The geometric mean sum concentrations of the most prevalent PBDE congeners (BDE-28, BDE-47, BDE-99, BDE-100, and BDE-153) were 22 ng/g lipid in winter 2010, 23 ng/g lipid in summer 2010, and 19 ng/g lipid in winter 2011. BDE-47 was the predominant congener. Based on a multivariable mixed regression model, we estimated that on average, a 1-ng/g serum increase in BDE-47 was associated with a 2.6-μg/dL decrease in total thyroxine (T4) (95% CI: –4.7, –0.35). Total T4 was inversely associated with each PBDE congener. Serum concentrations of PBDEs were not strongly associated with total triiodothyronine (T3), free T4, or thyroid-stimulating hormone (TSH). Conclusion: These results are consistent with those from animal studies showing that exposure to PBDEs is associated with a decrease in serum T4. Because the other TH concentrations did not appear to be associated with BDE exposures, our findings do not indicate effects on the pituitary–thyroid axis. Taken together, our findings suggest that PBDE exposure might decrease the binding of T4 to serum T4 binding proteins. Citation: Makey CM, McClean MD, Braverman LE, Pearce EN, He XM, Sjödin A, Weinberg JM, Webster TF. 2016. Polybrominated diphenyl ether exposure and thyroid function tests in North American adults. Environ Health Perspect 124:420–425; http://dx.doi. org/10.1289/ehp.1509755
Metabonomic Profiles Delineate the Effect of Traditional Chinese Medicine Sini Decoction on Myocardial Infarction in Rats

Background In spite of great advances in target-oriented Western medicine for treating myocardial infarction (MI), it is still a leading cause of death in a worldwide epidemic. In contrast to Western medicine, Traditional Chinese medicine (TCM) uses a holistic and synergistic approach to restore the balance of Yin-Yang of body energy so the body's normal function can be restored. Sini decoction (SND) is a well-known formula of TCM which has been used to treat MI for many years. However, its holistic activity evaluation and mechanistic understanding are still lacking due to its complex components. Methodology/Principal Findings A urinary metabonomic method based on nuclear magnetic resonance and ultra high-performance liquid chromatography coupled to mass spectrometry was developed to characterize MI-related metabolic profiles and delineate the effect of SND on MI. With Elastic Net for classification and selection of biomarkers, nineteen potential biomarkers in rat urine were screened out, primarily related to myocardial energy metabolism, including the glycolysis, citrate cycle, amino acid metabolism, purine metabolism and pyrimidine metabolism. With the altered metabolism pathways as possible drug targets, we systematically analyze the therapeutic effect of SND, which demonstrated that SND administration could provide satisfactory effect on MI through partially regulating the perturbed myocardial energy metabolism. Conclusions/Significance Our results showed that metabonomic approach offers a useful tool to identify MI-related biomarkers and provides a new methodological cue for systematically dissecting the underlying efficacies and mechanisms of TCM in treating MI.
Plasmonics-Based Refractive Index Sensor for Detection of Hemoglobin Concentration

An ultra-compact plasmonics-based sensor is investigated which is excited by Fano resonance. The structure is numerically simulated by the finite-difference time-domain method. The sensor utilizes unique waveguide geometry named as metal–insulator–metal (MIM) waveguide geometry which has an intriguing feature to confine signal far beyond diffraction light. Thus, it is used to devise ultra-compact optical circuits. The MIM waveguide is coupled to a pair of elliptical ring resonators and the interaction between the resonators excites special mode which is known as Fano resonance mode. It is a unique phenomenon which exhibits asymmetrical resonance profile and supports ultra narrow line width. Because of its exciting feature, a large value of sensitivity = 1100 nm/RIU and figure of merit = 224RIU−1 is obtained for the proposed sensor. The sensing performance of the device can be further enhanced by tailoring the geometrical parameters. The applicability of the device is also tested to detect the concentration of hemoglobin in blood. Thus, the device is well suited to design on-chip optical sensors.
SLAMM: Visual monocular SLAM with continuous mapping using multiple maps

This paper presents the concept of Simultaneous Localization and Multi-Mapping (SLAMM). It is a system that ensures continuous mapping and information preservation despite failures in tracking due to corrupted frames or sensor’s malfunction; making it suitable for real-world applications. It works with single or multiple robots. In a single robot scenario the algorithm generates a new map at the time of tracking failure, and later it merges maps at the event of loop closure. Similarly, maps generated from multiple robots are merged without prior knowledge of their relative poses; which makes this algorithm flexible. The system works in real time at frame-rate speed. The proposed approach was tested on the KITTI and TUM RGB-D public datasets and it showed superior results compared to the state-of-the-arts in calibrated visual monocular keyframe-based SLAM. The mean tracking time is around 22 milliseconds. The initialization is twice as fast as it is in ORB-SLAM, and the retrieved map can reach up to 90 percent more in terms of information preservation depending on tracking loss and loop closure events. For the benefit of the community, the source code along with a framework to be run with Bebop drone are made available at https://github.com/hdaoud/ORBSLAMM.
Children's Growth in an Adaptive Framework: Explaining the Growth Patterns of American Slaves and Other Historical Populations

This paper presents a new adaptive framework for understanding children's growth in the past. Drawing upon the recent work of Gluckman and Hanson (2006) and their co-authors on adaptive responses in relation to growth, I present three prenatal and three postnatal adaptive mechanisms that affect the growth patterns of children. The most novel adaptive response to the historical literature is the prenatal predictive adaptive response where the foetus develops assuming that the postnatal environment will closely match prenatal conditions. Thus, the metalbolism and growth trajectory of a child is programmed during the prenatal period: children experiencing good conditions in utero would have a higher metabolism and growth trajectory than their counterparts facing poor conditions. Having discussed the framework and other responses in detail, I then use it to reinterpret the growth pattern of American slaves (Steckel, 1979, 1986). I argue that the mismatch between relatively good conditions in utero and absolutely appalling conditions in infancy and early childhood led slave children to become incredibly stunted by age three or four. However, after this age, slave children experienced rapid catch-up growth, first because their immune systems had become more developed and had adapted to the poor disease environment and later because their diet improved tremendously and hookworm exposure was reduced when they entered the labour force around age ten. Thus, American slave children were able to experience rapid catch-up growth because they were prenatally programmed for a higher metabolism and growth trajectory. The paper concludes by setting out some stylized facts about children's growth in the past and pointing toward areas of future research.