Miracle-dz/UniFAR-FTUs huggingface dataset:
Wallace's line revisited: has vicariance or dispersal shaped the distribution of Malesian hawkmoths (Lepidoptera: Sphingidae)

Large-scale biogeographical patterns of Sphingidae in the Malesian archipelago are investigated, using Geographic Information System-supported estimates of species ranges determined from a compilation of specimen-label databases. Distribution maps for all species and checklists for 114 islands are presented at http://www.sphingidae- sea.biozentrum. uni-wuerzburg.de. Phenetic analyses of island faunas reveal 'textbook'-like patterns of biogeograph- ical associations in the region, with Wallace's line emerging as the main faunal discontinuity in the region. Further analyses, using partial Mantel statistics, indicate that historical features of geography (such as land bridges formed during periods of lower sea levels) are an important determinant of faunal similarity, but recent dispersal can also explain a significant portion of present day hawkmoth distributions. Faunal turnover in relation to distance between islands is steeper for Smerinthinae than for other subfamilies, indicating different dispersal abilities among higher taxonomic groups. These differences are discussed in the light of life-history differences between the subfamilies. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 455-468.
DimBoost: Boosting Gradient Boosting Decision Tree to Higher Dimensions

Gradient boosting decision tree (GBDT) is one of the most popular machine learning models widely used in both academia and industry. Although GBDT has been widely supported by existing systems such as XGBoost, LightGBM, and MLlib, one system bottleneck appears when the dimensionality of the data becomes high. As a result, when we tried to support our industrial partner on datasets of the dimension up to 330K, we observed suboptimal performance for all these aforementioned systems. In this paper, we ask "Can we build a scalable GBDT training system whose performance scales better with respect to dimensionality of the data? " The first contribution of this paper is a careful investigation of existing systems by developing a performance model with respect to the dimensionality of the data. We find that the collective communication operations in many existing systems only implement the algorithm designed for small messages. By just fixing this problem, we are able to speed up these systems by up to 2X. Our second contribution is a series of optimizations to further optimize the performance of collective communications. These optimizations include a task scheduler, a two-phase split finding method, and low-precision gradient histograms. Our third contribution is a sparsity-aware algorithm to build gradient histograms and a novel index structure to build histograms in parallel. We implement these optimizations in DimBoost and show that it can be 2-9X faster than existing systems.
Matrix metalloproteinase-9 in the pathophysiology and diagnosis of dry eye syndrome

: Dry eye and tear dysfunction are common ocular disorders that cause cornea barrier disruption resulting in a poorly lubricated and irregular cornea epithelium, eye irritation and blurred vision. Increased levels and activities of matrix metalloproteinases (MMPs), particularly MMP-9, have been detected in the tears and ocular surface epithelial and inflammatory cells in dry eye. MMPs have been found to participate in disruption of tight junctions in the apical cornea epithelium leading to their accelerated desquamation and barrier disruption. This review summarizes evidence showing the contribution of MMPs to dry eye pathogenesis and their roles as biomarkers and therapeutic targets.
Bushen Huoxue Recipe Alleviates Implantation Loss in Mice by Enhancing Estrogen–Progesterone Signals and Promoting Decidual Angiogenesis Through FGF2 During Early Pregnancy

Bushen Huoxue recipe (BSHXR) is a classic Chinese herbal prescription for nourishing the kidney and activating blood circulation. It consists of six herbs: Astragali radix, Angelicae sinensis radix, Ligustici Chuanxiong Rhizoma, Cuscutae semen, Taxilli Herba, and Dipsaci Radix, and the main active constituents of BSHXR are ferulic acid, calycosin-7-glucopyranoside, hyperoside, quercitrin, and asperosaponin VI. In clinical practice, BSHXR is traditionally used to treat failed pregnancy and its complications. However, little is known about the underlying mechanism of BSHXR for the treatment of implantation loss during early pregnancy. In the current study, controlled ovarian hyperstimulation was induced in mice as our implantation loss model, and we evaluated the effects of BSHXR on implantation, decidualization, decidual angiogenesis, and reproductive outcome. We showed that BSHXR could regulate the supraphysiological levels of serum estrogen and progesterone observed in these mice, and also act on estrogen and progesterone receptors in the stroma and epithelium. BSHXR also enhanced FGF2 expression in the vascular sinus folding area of the decidua, thus potentially reducing implantation loss during early pregnancy and contributing to placentation and survival of the fetuses. Taken together, our findings provide scientific evidence for the application of BSHXR in the clinic as a treatment for implantation loss during early pregnancy, and warrant further investigation of BSHXR as an effective treatment for failed pregnancy and its complications.
The Interaction of Ability Differences and Guessing When Modeling Differential Item Functioning With the Rasch Model

In educational testing, differential item functioning (DIF) statistics must be accurately estimated to ensure the appropriate items are flagged for inspection or removal. This study showed how using the Rasch model to estimate DIF may introduce considerable bias in the results when there are large group differences in ability (impact) and the data follow a three-parameter logistic model. With large group ability differences, difficult non-DIF items appeared to favor the focal group and easy non-DIF items appeared to favor the reference group. Correspondingly, the effect sizes for DIF items were biased. These effects were mitigated when data were coded as missing for item–examinee encounters in which the person measure was considerably lower than the item location. Explanation of these results is provided by illustrating how the item response function becomes differentially distorted by guessing depending on the groups’ ability distributions. In terms of practical implications, results suggest that measurement practitioners should not trust the DIF estimates from the Rasch model when there is a large difference in ability and examinees are potentially able to answer items correctly by guessing, unless data from examinees poorly matched to the item difficulty are coded as missing.
Alternative Carrier Solvents for Pigments Extracted from Spalting Fungi

The use of both naturally occurring and synthetic pigmented wood has been prevalent in woodcraft for centuries. Modern manifestations generally involve either woodworkers’ aniline dyes, or pigments derived from a special class of fungi known as spalting fungi. While fungal pigments are more renewable than anilines and pose less of an environmental risk, the carrier required for these pigments—dichloromethane (DCM)—is both problematic for humans and tends to only deposit the pigments on the surface of wood instead of evenly within the material. Internal coloration of wood is key to adoption of a pigmenting system by woodworkers. To address this issue, five solvents that had moderate solubility with the pigments extracted from Chlorociboria aeruginosa and Scytalidium cuboideum were identified, in the hopes that a reduction in solubility would result in a greater amount of the pigment deposited inside the wood. Of the tested solvents, acetonitrile was found to produce the highest internal color in ash, Douglas-fir, madrone, mountain hemlock, Port-Orford cedar, Pacific silver fir, red alder and sugar maple. While these carrier solvents are not ideal for extracting the pigments from the fungi, acetonitrile in particular does appear to allow for more pigment to be deposited within wood. The use of acetonitrile over DCM offers new opportunities for possible industrial spalting applications, in which larger pieces of wood could be uniformly pigmented and sold to the end user in larger quantities than are currently available with spalted wood.
Evaluation of an internal control in a multiplex-PCR assay for sex determination of in vitro -produced bovine embryos

The use of an internal control in a multiplex-PCR assay for sex determination of In Vitro-produced bovine embryos was evaluated in biopsies of groups of 54 fresh and 44 frozen embryos. The internal controls used were the primers BOV 1 and BOV 2, which amplify a product with 626 base pairs (bp) of bovine mitochondrial DNA ND5 gene. The primers BRY.4aF and BRY.4aR were used for bovine Y chromosome sequence amplification. The specificity of multiplex- PCR reactions realized in biopsies corresponding to about 20% of each fresh embryo (10 male and 10 female) by means of confirming the sexing in the remaining embryo content (~80%) presented 100% specificity. Amplicons of the internal control and Y chromosome were both amplified until dilution corresponding to 6.25% of total extracted DNA from a male embryo. Sex determination was possible in 53 (98.1%) fresh embryos and 40 (90.9%) frozen embryos. The products related to the Y chromosome and mitochondrial DNA were simultaneously amplified in 34 (63%) fresh embryos and 27 (61.4%) frozen embryos, showing a male embryo. The female sex, distinguished by internal control amplification only, was detected in 19 (35.2%) and 13 (29.5%) biopsies, respectively, of fresh and frozen embryos. In one (1.8%) and four (9.1%) biopsies of fresh and frozen embryos, respectively, neither product was amplified, most likely due to the absence of embryonic cells or the presence of embryonic cells going through apoptosis. The multiplex-PCR assay developed in this work showed avoided the limitation of a lack of an internal standard, and was also sensitive, specific, and efficient in reaction failure identification. This technique shows great potential for use on a commercial scale in routine sex determination of In Vitro-produced embryos.
Levetiracetam use during pregnancy in women with epilepsy: Preliminary observations from a tertiary care center in Northern India

INTRODUCTION: Data on efficacy and safety of levetiracetam (LEV) during pregnancy is still limited. We analyzed efficacy and safety of LEV during pregnancy in North Indian women with epilepsy (WWE) which is being presented here. PATIENTS AND METHODS: This retrospective study included 99 WWE (on treatment with a single antiepileptic drug [AED]) who were evaluated in medical-surgical disorder antenatal clinic of the department of obstetrics and gynecology at a tertiary care teaching hospital and referral center in North India. All the obstetric and fetal data as well as data pertaining to epilepsy were noted meticulously. RESULTS: In this study (n = 99), 35 women received carbamazepine, 28 received LEV, 15 received valproate (VPA), 13 received phenytoin (PHT), three each received oxcarbazepine and lamotrigine, respectively, and two received clobazam. Although the use of VPA was associated with significantly better control of seizures compared to LEV, its use was associated with higher risk of major congenital malformations (13.3%). The incidence of gestational hypertension was lower while incidence of fetal distress was significantly higher in WWE receiving PHT during pregnancy. None of the child born to pregnant women receiving LEV had any congenital malformation. CONCLUSION: LEV is a first-line AED during pregnancy. Future prospective studies using therapeutic drug monitoring during pregnancy may further help in establishing its role during pregnancy.
The role of model and initial condition error in numerical weather forecasting investigated with an observing system simulation experiment

A series of experiments that explore the roles of model and initial condition error in numerical weather prediction are performed using an observing system simulation experiment (OSSE) framework developed at the National Aeronautics and Space Administration Global Modeling and Assimilation Office (NASA/GMAO). The use of an OSSE allows the analysis and forecast errors to be explicitly calculated, and different hypothetical observing networks can be tested with ease. In these experiments, both a full global OSSE framework and an ‘identical twin’ OSSE setup are used to compare the behaviour of the data assimilation system (DAS) and evolution of forecast skill with and without model error. The initial condition error is manipulated by varying the distribution and quality of the observing network and the magnitude of observation errors. The results show that model error has a strong impact on both the quality of the analysis field and the evolution of forecast skill, including both systematic and unsystematic model error components. With a realistic observing network, the analysis state retains a significant quantity of error due to systematic model error. If errors of the analysis state are minimised, model error acts to rapidly degrade forecast skill during the first 24–48 hours of forward integration. In the presence of model error, the impact of observation errors on forecast skill is small, but in the absence of model error, observation errors cause a substantial degradation of the skill of medium-range forecasts.
Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes

Plant-parasitic nematodes cause considerable damage to crop plants. The rhizosphere microbiome can affect invasion and reproductive success of plant-parasitic nematodes, thus affecting plant damage. In this study, we investigated how the transplanted rhizosphere microbiome from different crops affect plant-parasitic nematodes on soybean or tomato, and whether the plant’s own microbiome from the rhizosphere protects it better than the microbiome from fallow soil. Soybean plants growing in sterilized substrate were inoculated with the microbiome extracted from the rhizosphere of soybean, maize, or tomato. Controls were inoculated with extracts from bulk soil, or not inoculated. After the microbiome was established, the root lesion nematode Pratylenchus penetrans was added. Root invasion of P. penetrans was significantly reduced on soybean plants inoculated with the microbiome from maize or soybean compared to tomato or bulk soil, or the uninoculated control. In the analogous experiment with tomato plants inoculated with either P. penetrans or the root knot nematode Meloidogyne incognita, the rhizosphere microbiomes of maize and tomato reduced root invasion by P. penetrans and M. incognita compared to microbiomes from soybean or bulk soil. Reproduction of M. incognita on tomato followed the same trend, and it was best suppressed by the tomato rhizosphere microbiome. In split-root experiments with soybean and tomato plants, a systemic effect of the inoculated rhizosphere microbiomes on root invasion of P. penetrans was shown. Furthermore, some transplanted microbiomes slightly enhanced plant growth compared to uninoculated plants. The microbiomes from maize rhizosphere and bulk soil increased the fresh weights of roots and shoots of soybean plants, and microbiomes from soybean rhizosphere and bulk soil increased the fresh weights of roots and shoots of tomato plants. Nematode invasion did not affect plant growth in these short-term experiments. In conclusion, this study highlights the importance of the rhizosphere microbiome in protecting crops against plant-parasitic nematodes. An effect of pre-crops on the rhizosphere microbiome might be harnessed to enhance the resistance of crops towards plant-parasitic nematodes. However, nematode-suppressive effects of a particular microbiome may not necessarily coincide with improvement of plant growth in the absence of plant-parasitic nematodes.
Emerging Adulthood Kimberley Radmacher and Margarita Azmitia ' ' Invisible ' ' Identity Unmasking Class : How Upwardly Mobile Poor and Working-Class Emerging Adults Negotiate an

This study examined class identity negotiation among upwardly mobile poor and working-class emerging adults. Twenty-one ethnically diverse emerging adults narrated class-related experiences during interviews about their transition to college. Narratives were coded for (1) the strategies emerging adults used to make sense of their class experiences and (2) the events that prompted their class identity negotiation. Participants used class identity management strategies that reflected dissociation or resistance. Cross-class interactions that involved recognition of financial and behavioral disparities between themselves and their professional class peers were more likely to trigger both dissociation and resistance strategies. In contrast, noncomparative class-related experiences (e.g., parent loss of job) and same-class interactions were more likely to elicit dissociation strategies. These findings highlight the struggle and feelings of ambivalence that upwardly mobile emerging adults face as they manage the stigma and discrimination associated with their class background and protect their self-esteem.
Trends in breast reconstruction: Implications for the National Health Insurance Service

Background Breast reconstruction has become more common as mastectomy has become more frequent. In Korea, the National Health Insurance Service (NHIS) began covering breast reconstruction in April 2015. This study aimed to investigate trends in mastectomy and breast reconstruction over the past 10 years and to evaluate the impact of NHIS coverage on breast reconstruction. Methods Nationwide data regarding mastectomy and breast reconstruction were collected from the Korean Breast Cancer Society registry database. Multiple variables were analyzed in the records of patients who underwent breast reconstruction from January 2005 to March 2017 at a single institution. Results At Seoul National University Hospital, the total number of reconstruction cases increased 13-fold from 2005 to 2016. The proportion of immediate breast reconstruction (IBR) cases out of all cases of total mastectomy increased from 4% in 2005 to 52.0% in 2016. The proportion of delayed breast reconstruction (DBR) cases out of all cases of breast reconstruction and the overall number of DBR cases increased from 8.8% (20 cases) in 2012 to 18.3% (76 cases) in 2016. After NHIS coverage was initiated, the proportions of IBR and DBR showed statistically significant increases (P<0.05). Among the IBR cases, the percentage of prosthesis-based reconstructions increased significantly (P<0.05), but this trend was not found with DBR. Total mastectomy became significantly more common after the expansion of NHIS coverage (P<0.05). Conclusions Over the last decade, there has been an increase in mastectomy and breast reconstruction, and the pace of increase accelerated after the expansion of NHIS coverage. It is expected that breast reconstruction will be a routine option for patients with breast cancer under the NHIS.
Serum Sclerostin as a Possible Biomarker in Ankylosing Spondylitis: A Case-Control Study

Objective Several molecules are involved in the pathogenesis of a new bone formation in ankylosing spondylitis (AS). The aim of this study was to evaluate the serum levels of sclerostin in patients with AS as a possible biomarker and to investigate any correlations with radiographic damage, disease activity, and function. Methods AS patients fulfilled the modified New York criteria, and healthy controls were enrolled for this study. BASDAI, ASDAS-CRP, BASMI, BASFI, patient and physician VAS, and C-reactive protein were evaluated at baseline visit. Spinal damage was assessed using the mSASSS on radiographs performed within 3 months from baseline. Serum concentrations of sclerostin were assessed at baseline and after four months of therapy in patients who started an anti-TNF. Results Twenty healthy subjects and 40 AS patients were enrolled in the study. In our group, serum sclerostin levels (median (25th–75th percentile)) were significantly higher in healthy controls (18.04 (13.6–24) pg/ml) than in AS patients (6.46 (4.5–11.1) pg/ml; P value < 0.01). However, no significant correlations were found between serum sclerostin levels and radiographic damage, assessed by mSASSS, and between serum sclerostin levels and clinical indices of activity and disability or with laboratory parameters. Sclerostin levels did not show significant changes after 4 months of anti-TNF therapy. Conclusions The results of our study suggest a possible role of sclerostin in the identification of AS patients. Further studies are needed to prove the role of sclerostin as a disease activity biomarker and progression of disease in AS.
Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitogenome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species that distribute across different climates. We sequenced 26 complete mitogenomes of Tetranychus truncates, which occurs in both warm and cold regions, and nine complete mitogenomes of Tetranychus pueraricola, which is restricted to warm regions. Patterns of evolution in the two species’ mitogenomes were compared through a series of dN/dS methods and physicochemical profiles of amino acid replacements. We found that: (1) the mitogenomes of both species were under widespread purifying selection; (2) elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus; and (3) the strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation.
Detecting Influential Nodes Incrementally and Evolutionarily in Online Social Networks

Detecting influential nodes and understanding their evolution patterns are very important for information diffusion in online social networks. Although some work has been done in literature, it is still not clear that: (1) how to measure the influential degree of nodes for information diffusion, and (2) how influential nodes evolve during the diffusion process. To address the two challenges, we identify an incremental approach to measuring users’ influential degrees, detecting local and global influential nodes, and analyzing their evolution patterns, for which we propose three methods to partition time window. The three methods are the uniform time window, the non-uniform time window, and the uniform retweets number window, respectively. We apply our model on real data set in Sina weibo and conduct extensive analyses, from which we gain several interesting findings. We also validate the effects of our method, by comparing the influence spread with our detected influential nodes as seeds, to other seed selection algorithms, which shows that our work has better performance.