Miracle-dz/UniFAR-FTUs huggingface dataset:
Explain Yourself: A Natural Language Interface for Scrutable Autonomous Robots

Autonomous systems in remote locations have a high degree of autonomy and there is a need to explain what they are doing and why in order to increase transparency and maintain trust. Here, we describe a natural language chat interface that enables vehicle behaviour to be queried by the user. We obtain an interpretable model of autonomy through having an expert 'speak out-loud' and provide explanations during a mission. This approach is agnostic to the type of autonomy model and as expert and operator are from the same user-group, we predict that these explanations will align well with the operator's mental model, increase transparency and assist with operator training.
A modified Essen Stroke Risk Score for predicting recurrent ischemic stroke at one year

Abstract Objective The Essen Stroke Risk Score (ESRS) is widely used to predict the risk of recurrent ischemic stroke but may not have sufficient discriminatory ability for predicting early recurrence. In this study, we developed a modified ESRS for predicting recurrent ischemic stroke at one year based on Chinese population. Methods Eight hundred and three consecutive patients were included in the study. We performed a univariate analysis to investigate the effect of previously identified risk factors on recurrent stroke at one year. The candidate predictors were included in a forward stepwise logistic regression model. Prediction scores were assigned based on β coefficient and a modified ESRS system was constructed. We used receiver operating characteristic (ROC) curves to compare the predictive ability of the modified and original ESRS. Results Recurrent ischemic stroke occurred in 85 (11.00%) patients and death occurred in 68 (8.80%) patients within one year. Hypertension over 15 years, diabetes over 10 years, large artery atherosclerosis cerebral infarction by TOAST criteria and a history of transient ischemic attack (TIA) or ischemic stroke (IS) were identified as independent risk factors for recurrent stroke (all P < 0.05). The areas under the ROC curves of ESRS and modified ESRS were 0.58 (P < 0.05, 95%CI: 0.51–0.64) and 0.70 (P < 0.05, 95% CI: 0.63–0.76), respectively. The modified ESRS appears to be superior to the original ESRS for predicting recurrent ischemic stroke at one year (P < 0.05). Conclusions The modified ESRS increased the ability of the original ESRS to predict recurrent stroke at one year among the Chinese population.
Unsupervised Coreference Resolution with HyperGraph Partitioning

Unsupervised-learning based coreference resolution obviates the need for annotation of training data. However, unsupervised approaches have traditionally been relying on the use of mention-pair models, which only consider information pertaining to a pair of mentions at a time. In this paper, it is proposed the use of hypergraph partitioning to overcome this limitation. The mentions are modeled as vertices. By allowing a hyperedge to cover multiple mentions that share a common property, the additional information beyond a mention pair can be captured. This paper introduces a hypergraph partitioning algorithm that divides mentions directly into equivalence classes representing individual entities. Evaluation on the ACE dataset shows that our unsupervised hypergraph based approach outperforms previous unsupervised methods.
Assessing the Value of Prehabilitation in Patients Undergoing Colorectal Surgery According to the Enhanced Recovery After Surgery (ERAS) Pathway for the Improvement of Postoperative Outcomes: Protocol for a Randomized Controlled Trial

Background A key element in the postoperative phase of the standardized Enhanced Recovery After Surgery (ERAS) treatment pathways is mobilization. Currently, there are no recommendations in the ERAS guidelines for preoperative physical activity. Patients undergoing major surgery are prone to functional decline due to the impairment of muscle, cardiorespiratory, and neurological function as a response to surgical stress. It has been shown that preoperative physical training reduces postoperative complications. To date, there are limited studies that investigate preoperative physical training combined with ERAS. Objective The aim of this study is to assess the impact of tailored physical training prior to colorectal surgery conducted according to an ERAS protocol on overall morbidity. This study proposes the initial hypothesis that 3-6 weeks of prehabilitation before elective colorectal surgery may improve postoperative outcome and reduce complication rates, assessed using the Comprehensive Complication Index. The primary objective is to evaluate overall morbidity due to postoperative complications. Additionally, complications are assessed according to the Clavien-Dindo classification, length of stay, readmission rate, mortality rate, and treatment-related costs. Methods The prehabilitation Enhanced Recovery After colorectal Surgery (pERACS) study is a single-center, single-blinded prospective randomized controlled trial. Patients scheduled for colorectal resections are randomly assigned either to the prehabilitation group or the control group. All patients are treated with the ERAS pathway for colorectal resections according to a standardized study schedule. Sample size calculation performed by estimating a clinically relevant 25% reduction of postoperative complications (alpha=.05, power 80%, dropout rate of 10%) resulted in 56 randomized patients per group. Results Following ethical approval of the study protocol, the first patient was included in June 2016. At this time, a total of 40 patients have been included; 27 patients terminated the study by the end of March 2017. Results are expected to be published in 2018. Conclusions The pERACS trial is a single-center, single-blinded prospective randomized controlled trial to assess the impact of tailored physical training prior to colorectal surgery, conducted according to an ERAS protocol, in order to evaluate overall morbidity. Trial Registration Clinicaltrials.gov NCT02746731; https://clinicaltrials.gov/ct2/show/NCT02746731 (Archived by WebCite at http://www.webcitation.org/6tzblGwge)
Neoadjuvant chemotherapy followed by radiotherapy and concurrent hyperthermia in patients with advanced-stage cervical cancer: A retrospective study

Objective: To evaluate the efficacy of neoadjuvant chemotherapy, followed by radiotherapy and concurrent hyperthermia (triple therapy) in patients with advanced-stage cervical cancer. Methods: We selected 43 patients from our hyperthermia database, who were treated from 1996 to 2010 with triple therapy for large primary tumours (>6 cm) or para-aortic lymph node metastases. All patients received platinum-based chemotherapy followed by full-dose radiotherapy, brachytherapy and five hyperthermia treatments. The response was evaluated by gynaecological examination and a CT-scan. Time-to-event variables were estimated using the Kaplan Meier method and the Cox regression method. Results: The mean age of the patients was 50.4 years (range 29–80). The median tumour size was 5.6 cm at diagnosis (range 2.6–8.2), positive lymph nodes were present in 90.7%. A total of 67% of the patients completed all six planned courses of chemotherapy. After completion of neoadjuvant chemotherapy, 83.7% of patients achieved a complete or partial response. At the end of treatment, the complete response rate was 81.4% (95%CI 69.2–93.5). Grade 2, 3 and 4 acute vascular toxicity occurred in 17 patients. The incidence of grade 3–4 haematological toxicity did not exceed 10% and no neutropenic fever occurred. For grade 1–2 renal toxicity, a switch to carboplatin was made (n = 6). No acute grade 3–4 renal toxicity was observed. No treatment-related deaths were recorded. The median follow-up time was 29.8 months (range 4.1–124.8). Overall survival rate at 12 months was 79% (95%CI 57.4–92.3). Conclusion: The triple therapy seems feasible and effective in the treatment of advanced-stage, high-risk cervical cancer. However, chemotherapy-induced vascular toxicity occurred frequently, which may warrant the use of prophylactic anticoagulants. We recommend a phase II trial for prospective confirmation for comparison with standard chemoradiation and the use of anticoagulants.
Energy efficiency of data center operating practices: Server clustering, powering on/off, and bang–bang control

Data centers today account for up to 3% of all global electricity consumption and produce 200 million metric tons of CO 2 . Hence, improving energy efficiency is an important operational concern. This article examines common operating practices such as server clustering, powering on/off, and bang–bang control in terms of energy efficiency. Extending the mixed integer programming (MIP) formulation in a previous research study, we introduce new constraints reflecting the operating practices adopted for operational convenience. We develop an algorithmic strategy for constructing energy efficient clusters of servers using two upper bounds on the cluster size. Numerical experiments show that server clustering and bang–bang control do not diminish energy efficiency, and that powering on/off by itself is insufficient. Our results produce a conclusion that differs from the published literature on data center design and operations. © 2017 Wiley Periodicals, Inc. NETWORKS, Vol. 71(2), 107–119 2018
Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo

ABSTRACT The euryhaline cyanobacterium Synechococcus sp. strain PCC 7002 has an obligate requirement for exogenous vitamin B12 (cobalamin), but little is known about the roles of this compound in cyanobacteria. Bioinformatic analyses suggest that only the terminal enzyme in methionine biosynthesis, methionine synthase, requires cobalamin as a coenzyme in Synechococcus sp. strain PCC 7002. Methionine synthase (MetH) catalyzes the transfer of a methyl group from N5-methyl-5,6,7,8-tetrahydrofolate to l-homocysteine during l-methionine synthesis and uses methylcobalamin as an intermediate methyl donor. Numerous bacteria and plants alternatively employ a cobalamin-independent methionine synthase isozyme, MetE, that catalyzes the same methyl transfer reaction as MetH but uses N5-methyl-5,6,7,8-tetrahydrofolate directly as the methyl donor. The cobalamin auxotrophy of Synechococcus sp. strain PCC 7002 was complemented by using the metE gene from the closely related cyanobacterium Synechococcus sp. strain PCC 73109, which possesses genes for both methionine synthases. This result suggests that methionine biosynthesis is probably the sole use of cobalamin in Synechococcus sp. strain PCC 7002. Furthermore, a cobalamin-repressible gene expression system was developed in Synechococcus sp. strain PCC 7002 that was used to validate the presence of a cobalamin riboswitch in the promoter region of metE from Synechococcus sp. strain PCC 73109. This riboswitch acts as a cobalamin-dependent transcriptional attenuator for metE in that organism. IMPORTANCE Synechococcus sp. strain PCC 7002 is a cobalamin auxotroph because, like eukaryotic marine algae, it uses a cobalamin-dependent methionine synthase (MetH) for the final step of l-methionine biosynthesis but cannot synthesize cobalamin de novo. Heterologous expression of metE, encoding cobalamin-independent methionine synthase, from Synechococcus sp. strain PCC 73109, relieved this auxotrophy and enabled the construction of a truly autotrophic Synechococcus sp. strain PCC 7002 more suitable for large-scale industrial applications. Characterization of a cobalamin riboswitch expands the genetic toolbox for Synechococcus sp. strain PCC 7002 by providing a cobalamin-repressible expression system.
Investigation of cBN Electroplated End-Mill Shape for CFRP Machining

Currently, carbon fiber reinforced plastics (CFRP) are being increasingly adopted in various fields. Thus, machining CFRP with high accuracy and high efficiency is required. In addition, machining stack materials composed of CFRP and titanium alloys is required. Therefore, in this study, a novel end-mill electroplated with a cubic boron nitride (cBN) abrasive, which has high thermal resistance, is proposed. In order to evaluate the influence of the base metal shape of the proposed end-mill on the machining process, several cBN-electroplated end-mills with different rake angles or chamfers were fabricated and used to cut CFRP. In addition, in order to evaluate the abrasive shape, a blocky abrasive was also electroplated on the end-mill. The results indicate that the negative rake angle is useful to restrain the progression of tool wear. However, in order to obtain the element of cutting and grinding, it is required that the rake angle should be positive. Moreover, the reasonable width of chamfer is effective for restraining the increase in CFRP temperature. Further, a sharp shaped abrasive can more effectively generate a CFRP with a sharp edge compared with a blocky shape abrasive.
Hfq and three Hfq‐dependent small regulatory RNAs—MgrR, RyhB and McaS—coregulate the locus of enterocyte effacement in enteropathogenic Escherichia coli

&NA; Enteropathogenic Escherichia coli (EPEC) is a significant cause of infantile diarrhea and death in developing countries. The pathogenicity island locus of enterocyte effacement (LEE) is essential for EPEC to cause diarrhea. Besides EPEC, the LEE is also present in other gastrointestinal pathogens, most notably enterohemorrhagic E. coli (EHEC). Whereas transcriptional control of the LEE has been meticulously examined, posttranscriptional regulation, including the role of Hfq‐dependent small RNAs, remains undercharacterized. However, the past few years have witnessed a surge in the identification of riboregulators of the LEE in EHEC. Contrastingly, the posttranscriptional regulatory landscape of EPEC remains cryptic. Here we demonstrate that the RNA‐chaperone Hfq represses the LEE of EPEC by targeting the 5′ untranslated leader region of grlR in the grlRA mRNA. Three conserved small regulatory RNAs (sRNAs)—MgrR, RyhB and McaS—are involved in the Hfq‐dependent regulation of grlRA. MgrR and RyhB exert their effects by directly base‐pairing to the 5′ region of grlR. Whereas MgrR selectively represses grlR but activates grlA, RyhB represses gene expression from the entire grlRA transcript. Meanwhile, McaS appears to target the grlRA mRNA indirectly. Thus, our results provide the first definitive evidence that implicates multiple sRNAs in regulating the LEE and the resulting virulence of EPEC. &NA; Graphical Abstract Figure. This manuscript describes identification of the first regulatory small RNAs that control the virulence of enteropathogenic Escherichia coli.
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
Acquired resistance to BRAF inhibition in BRAFV600E mutant gliomas

Activating mutation of BRAF is a common finding in pediatric gliomas. As many as 14% of high grade and up to 66% of certain subtypes of low grade pediatric glioma have the BRAFV600E mutation. Small molecule inhibitors that selectively target BRAFV600E are FDA approved for melanoma and have shown significant efficacy in treating BRAFV600E glioma in pre-clinical trials. Despite showing initial anti-tumor activity, acquired drug resistance significantly limits the benefit from being treated with BRAFV600E inhibitors. Here, we have identified molecular responses to BRAFV600E inhibitor treatment in human glioma models that have substantial clinical implications. Specifically, we show that BRAFV600E inhibitor resistant cells upregulate pro-survival mediators such as Wnt, and additionally increase receptor tyrosine kinase activity, including EGFR and Axl, promoting resistance to BRAFV600E inhibition. Our results suggest strategies to circumvent acquired resistance to BRAFV600E inhibitor therapy, and thereby improve outcomes for patients with BRAFV600E gliomas.
GSDS 2.0: an upgraded gene feature visualization server

Summary: Visualizing genes’ structure and annotated features helps biologists to investigate their function and evolution intuitively. The Gene Structure Display Server (GSDS) has been widely used by more than 60 000 users since its first publication in 2007. Here, we reported the upgraded GSDS 2.0 with a newly designed interface, supports for more types of annotation features and formats, as well as an integrated visual editor for editing the generated figure. Moreover, a user-specified phylogenetic tree can be added to facilitate further evolutionary analysis. The full source code is also available for downloading. Availability and implementation: Web server and source code are freely available at http://gsds.cbi. pku.edu. cn. Contact: gaog@mail.cbi. pku.edu. cn or gsds@mail.cbi. pku.edu. cn Supplementary information: Supplementary data are available at Bioinformatics online.
Descriptor : Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters , Ostrea lurida

Olympia oysters are found along the west coast of North America and as the only native oyster species in the region, receive considerable attention with regard to restoration and conservation. Knowledge of genetic structure of this species is essential for resource managers. Here we provide genetic data for three distinct populations of Olympia oysters in Puget Sound, Washington, USA in the form of genotype-bysequencing data (GBS). Specifically, this includes description of sequence data and a derived table that provides single nucleotide polymorphism (SNP) information for 10,363 loci. These data are valuable not only for resource managers responsible for restoration aquaculture practices, but can provide insight into ecological drivers of selection and diversity.
Improved Silver Optical Constants for Photovoltaic Plasmonics

Plasmonics open up new ways to construct optically thick but physically very thin photovoltaic absorbers. Silver is the most favored plasmonic material, and has demonstrated the lowest parasitic absorption losses among other noble metals. However, the presence of many different sets of optical constants for silver in literature makes it difficult to conduct reliable theoretical analysis. Realistic predictions necessitate optical constant data sets that are more accurate, considering that even small variations can influence calculation of Surface Plasmon effectiveness. Surface tarnish layers form quickly when silver is exposed to air making it challenging to determine the optical constants from air exposed samples. Our work aims to determine a reliable set of values that can be used with confidence in predicting experimental outcomes. We measured the optical data of silver using a novel method avoiding the air exposed side that might be contaminated. Our work seeks to pinpoint accurate values by using a range of different measurement approaches.
Early differences in fecal microbiota composition in children may predict overweight.

BACKGROUND Experimental studies suggest that gut microbiota deviations predispose toward energy storage and obesity. OBJECTIVE We wanted to establish whether early gut microbiota composition can guide weight development throughout early childhood. DESIGN Overweight and obese children (n = 25) were selected from a prospective follow-up study at the age of 7 y and identified according to the International Obesity Task Force criteria. Normal-weight children (n = 24) were selected from the same cohort and matched for gestational age and body mass index at birth, mode of delivery, probiotic supplementation, duration of breastfeeding, use of antibiotics during infancy, and frequencies of atopic diseases and atopic sensitization. Early fecal microbiota composition was analyzed by fluorescent in situ hybridization (FISH) with microscopic and flow cytometry detection and by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The bifidobacterial numbers in fecal samples during infancy, as assessed by the FISH with flow cytometry, were higher in children remaining normal weight, [median: 2.19 x 10(9) cells/g (interquartile range: 1.10-5.28 x 10(9) cells/g)] than in children becoming overweight [1.20 x 10(9) cells/g (0.48-1.59x 10(9) cells/g); P = 0.02]. A similar tendency was found by FISH with microscopic detection and qRT-PCR. The microbiota aberrancy during infancy in children becoming overweight was also associated with a greater number of Staphylococcus aureus [0.64 x 10(6) cells/g (0.33-1.00 x 10(6) cells/g)] than in children remaining normal weight [0.27 x 10(6) cells/g (0.17-0.50 x 10(6) cells/g); P = 0.013]. CONCLUSION Aberrant compositional development of the gut microbiota precedes overweight, offering new possibilities for preventive and therapeutic applications in weight management.
A Brandom-ian view of Reinforcement Learning towards strong-AI

The analytic philosophy of Robert Brandom, based on the ideas of pragmatism, paints a picture of sapience, through inferentialism. In this paper, we present a theory, that utilizes essential elements of Brandom's philosophy, towards the objective of achieving strong-AI. We do this by connecting the constitutive elements of reinforcement learning and the Game Of Giving and Asking For Reasons. Further, following Brandom's prescriptive thoughts, we restructure the popular reinforcement learning algorithm A3C, and show that RL algorithms can be tuned towards the objective of strong-AI.
Semiclassical solutions of generalized Wheeler-DeWitt cosmology

We consider an extension of Wheeler-DeWitt minisuperpace cosmology with additional interaction terms that preserve the linear structure of the theory. General perturbative methods are developed and applied to known semiclassical solutions for a closed Universe filled with a massless scalar. The exact Feynman propagator of the free theory is derived by means of a conformal transformation in minisuperspace. As an example, a stochastic interaction term is considered, and first order perturbative corrections are computed. It is argued that such an interaction can be used to describe the interaction of the cosmological background with the microscopic d.o. f. of the gravitational field. A Helmoltz-like equation is considered for the case of interactions that do not depend on the internal time, and the corresponding Green's kernel is obtained exactly. The possibility of linking this approach to fundamental theories of quantum gravity is investigated.