Miracle-dz/UniFAR-FTUs huggingface dataset:
A Field Sensor: computing the composition and intent of PubMed queries

Abstract PubMed® is a search engine providing access to a collection of over 27 million biomedical bibliographic records as of 2017. PubMed processes millions of queries a day, and understanding these queries is one of the main building blocks for successful information retrieval. In this work, we present Field Sensor, a domain-specific tool for understanding the composition and predicting the user intent of PubMed queries. Given a query, the Field Sensor infers a field for each token or sequence of tokens in a query in multi-step process that includes syntactic chunking, rule-based tagging and probabilistic field prediction. In this work, the fields of interest are those associated with (meta-)data elements of each PubMed record such as article title, abstract, author name(s), journal title, volume, issue, page and date. We evaluate the accuracy of our algorithm on a human-annotated corpus of 10 000 PubMed queries, as well as a new machine-annotated set of 103 000 PubMed queries. The Field Sensor achieves an accuracy of 93 and 91% on the two corresponding corpora and finds that nearly half of all searches are navigational (e.g. author searches, article title searches etc.) and half are informational (e.g. topical searches). The Field Sensor has been integrated into PubMed since June 2017 to detect informational queries for which results sorted by relevance can be suggested as an alternative to those sorted by the default date sort. In addition, the composition of PubMed queries as computed by the Field Sensor proves to be essential for understanding how users query PubMed.
Cladribine tablets added to IFN-β in active relapsing MS

Objective To evaluate the safety and efficacy of cladribine tablets in patients still experiencing active relapsing MS despite interferon (IFN)-β treatment. Methods A 96-week phase II study, randomizing patients treated with IFN-β to cladribine tablets 3.5 mg/kg/IFN-β or placebo/IFN-β. Patients were to receive cladribine tablets 3.5 mg/kg/IFN-β or placebo/IFN-β in a 2:1 ratio (n = 172) with safety and exploratory efficacy outcomes being assessed. Results Adverse events (AEs) and serious AEs were similar across treatment groups, except lymphopenia. Fifty of 124 (40.3%) cladribine/IFN-β recipients vs 0% of placebo/IFN-β recipients reported lymphopenia as an AE, with grade 3/4 lymphopenia (laboratory lymphocyte count < 500 cells/mm3) experienced by 79/124 (63.7%) vs 1 (2.1%), respectively. Patients treated with cladribine tablets 3.5 mg/kg/IFN-β were 63% less likely to have a qualifying relapse than placebo/IFN-β recipients, and cladribine tablets 3.5 mg/kg/IFN-β reduced most MRI measures of disease activity. Conclusions In patients with active relapsing MS despite IFN-β treatment, cladribine tablets 3.5 mg/kg/IFN-β reduced relapses and MRI lesion activity over 96 weeks compared with placebo/IFN-β but led to an increased incidence of lymphopenia. Classification of evidence This study provides Class I evidence that for patients with active relapsing MS despite IFN-β treatment, cladribine tablets added to IFN-β reduced relapses and MRI lesion activity over 96 weeks and increased the incidence of lymphopenia. Clinical trial registration NCT00436826.
When Do Gomory-Hu Subtrees Exist?

Gomory-Hu (GH) Trees are a classical sparsification technique for graph connectivity. It is also a fundamental model in combinatorial optimization which finds new applications, for instance , finding highly-connected communities within (social) networks. For any edge-capacitated undirected graph G = (V, E) and any subset of terminals Z ⊆ V , a Gomory-Hu Tree is an edge-capacitated tree T = (Z, E(T)) such that for every u, v ∈ Z, the value of the minimum capacity uv cut in G is the same as in T. It is well-known that we may not always find a GH tree which is a subgraph (or minor if Z = V) of G. For instance, every GH tree for the nodes of K 3,3 is a 5-star. We characterize those graph and terminal pairs (G, Z) which always admit such a tree. We show that these are the graphs which have no terminal-K 2,3 minor, that is, a K 2,3 minor each of whose nodes corresponds to a terminal of Z. We then show that the pairs (G, Z) which forbid such K 2,3 "Z-minors" arises, roughly speaking, from so-called Okamura-Seymour instances. These are planar graphs where the outside face contains all the terminals. This characterization yields an unexpected consequence for multiflow problems which extends an earlier line of inquiry due to Lomonosov and Seymour. Fix a graph G and subset Z ⊆ V (G) of terminals. Call (G, Z) cut-sufficient if the cut condition is sufficient to characterize the existence of a multiflow for any demands between nodes in Z, and any edge capacities on G. Then (G, Z) is cut-sufficient if and only if it is terminal-K 2,3 free.
Revisiting Cross Modal Retrieval

This paper proposes a cross-modal retrieval system that leverages on image and text encoding. Most multimodal architectures employ separate networks for each modality to capture the semantic relationship between them. However, in our work image-text encoding can achieve comparable results in terms of cross-modal retrieval without having to use a separate network for each modality. We show that text encodings can capture semantic relationships between multiple modalities. In our knowledge, this work is the first of its kind in terms of employing a single network and fused image-text embedding for cross-modal retrieval. We evaluate our approach on two famous multimodal datasets: MS-COCO and Flickr30K.
Probability and expected frequency of breakthroughs - a robust method of research assessment based on the double rank property of citation distributions

In research policy, effective measures that lead to improvements in the generation of knowledge must be based on reliable methods of research assessment, but for many countries and institutions this is not the case. Publication and citation analyses can be used to estimate the part played by countries and institutions in the global progress of knowledge, but a concrete method of estimation is far from evident. The challenge arises because publications that report real progress of knowledge form an extremely low proportion of all publications; in most countries and institutions such contributions appear less than once per year. One way to overcome this difficulty is to calculate probabilities instead of counting the rare events on which scientific progress is based. This study reviews and summarizes several recent publications, and adds new results that demonstrate that the citation distribution of normal publications allows the probability of the infrequent events that support the progress of knowledge to be calculated.
Extracts of Physalis peruviana Protect Astrocytic Cells Under Oxidative Stress With Rotenone

The use of medicinal plants to counteract the oxidative damage in neurodegenerative diseases has steadily increased over the last few years. However, the rationale for using these natural compounds and their therapeutic benefit are not well explored. In this study, we evaluated the effect of different Physalis peruviana extracts on astrocytic cells (T98G) subjected to oxidative damage induced by rotenone. Extracts of fresh and dehydrated fruits of the plant with different polarities were prepared and tested in vitro. Our results demonstrated that the ethanolic extract of fresh fruits (EF) and acetone-dehydrated fruit extract (AD) increased cell viability, reduced the formation of reactive oxygen species (ROS) and preserved mitochondrial membrane potential. In contrast, we observed a significant reduction in mitochondrial mass when rotenone-treated cells were co-treated with EF and AD. These effects were accompanied by a reduction in the percentage of cells with fragmented/condensed nuclei and increased expression of endogenous antioxidant defense survival proteins such as ERK1/2. In conclusion, our findings suggest that ethanolic and acetone extracts from P. peruviana are potential medicinal plant extracts to overcome oxidative damage induced by neurotoxic compounds.
Adjuvant radiation provides survival benefit for resected pancreatic adenocarcinomas of the tail.

Background The appropriate adjuvant treatment for resected pancreatic cancer remains a controversy. We sought to determine the effect of adjuvant treatment on overall survival (OS) in patients with pancreatic tail adenocarcinoma. Methods Retrospective review of patients with upfront surgically resected pancreatic tail cancer treated at our institution between 2000-2012 was performed to determine outcomes of patients treated with and without adjuvant radiation therapy (RT). Survival curves were calculated according to the Kaplan-Meier method. Univariate analysis (UVA) and multivariate analysis (MVA) were performed using the Cox proportional hazards model. Results Thirty-four patients met inclusion criteria. 79% received adjuvant chemotherapy, either concurrent with RT or alone. The groups were well matched, with the only significant difference being patient sex. On both UVA and MVA there was significantly worse survival in patients with a post-op CA19-9 >90 [hazard ratio (HR) 5.55; 95% confidence interval (CI): 1.20-25.7, P=0.03] and improved survival in patients treated with adjuvant RT (HR 0.15; 95% CI: 0.04-0.58, P=0.006). The median and 2-year OS were 21.6 months and 47% for patients treated with adjuvant RT compared with 11.3 months and 21% for those treated without RT. Conclusions Although few in patient numbers, this data suggests integration of adjuvant RT in resected pancreatic tail adenocarcinoma may improve OS.
Y Kuşağı Çalışanlarının Motivasyon Profillerinin Belirlenmesine Yönelik Bir Araştırma

Dunya genelinde ekonomik ve sosyal hareketlerle olusmus zaman araliklarina jenerasyon denmektedir. Yetisme tarzlari ve icinde bulunduklari ortam degisiklikleri nedeniyle “kusak” olarak da adlandirilan jenerasyonlar arasinda gerek karakter gerek calisma yontemleri ve gerekse isyerinden beklentilerde onemli farkliliklar gozlenebilmektedir. Farkli yas gruplarinin birarada calistigi gunumuz isyerlerinde yasanan sorunlarin onemli bir kismi kusaklararasi algi, yontem, uygulama ve iletisim farkliliklarindan kaynaklanmaktadir. Bu nedenle isletme yonetimleri, Y kusagi (1980 – 1999 arasi doganlar) calisanlarini gundemlerine alarak onlari kazanmaya calismak ve X kusagi (1965 – 1979 arasi doganlar) veya daha onceki kusaklardan olan yoneticilerini Y kusagi calisanlarini yonetecek sekilde gelistirmek konulari uzerinde daha cok durmaya baslamislardir. Arastirma nitel arastirma yaklasimlarindan katilimci gozlem ve yariyapilandirilmis gorusme teknigi ile gerceklestirilmis olup, veriler betimsel olarak cozumlenmistir. Elde edilen verilerin analizleri ile Y kusagi calisanlarinin is tatmini ve motivasyon saglayan faktorlerin neler olduguna yer verilmistir
Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species

The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.
Do Personality Features Influence Our Intuitions of the Mind-Body Problem? A Pilot Study

The elusive relationship between the mental domain and the physical brain, known as the mind-body problem, is still a hot topic of discussion among philosophers and neuroscientists. Rather than solving this problem, our pilot study addresses the question as to whether personality features could influence intuitions of the mind-body problem, or more precisely, whether it is possible to identify a person’s intuitive inclinations toward dualism or materialism and their inclinations toward reduction of the mind to the brain. For the purposes of this pilot study, we developed a questionnaire, which employed several theories of analytic philosophy of the mind, in order to determine which category the participants would belong to. These main categories were dualism, non-reductive materialism and reductive materialism. To test whether personality features affect preferences for these categories, the participants were investigated by Cloninger’s Temperament and Character Inventory (TCI). We found significant differences in the self-transcendence dimension of the TCI between participants who were evaluated as dualists and those who were assessed as reductive materialists. Our data show that the personality dimension of self-transcendence correlates with intuitive inclination toward reductive materialism or dualism. In addition, our results suggest that ideas, theories, and hypothetical solutions of the mind-body problem and possibly even conclusions, acceptance, and disputations of thought experiments of philosophy of the mind can be biased by personality traits. This fact should be taken into account in future discussions of the philosophy of the mind and may also be important for empirical research and an empirical understanding of the mind.
Super-Resolution Axial Localization of Ultrasound Scatter Using Multi-Focal Imaging

<italic>Objective:</italic> This paper aims to develop a method for achieving micrometre axial scatterer localization for medical ultrasound, surpassing the inherent, pulse length dependence limiting ultrasound imaging. <italic>Methods:</italic> The method, directly translated from cellular microscopy, is based on multi-focal imaging and the simple, aberration-dependent, image sharpness metric of a single point scatterer. The localization of a point scatterer relies on the generation of multiple overlapping sharpness curves, created by deploying three foci during receive processing, and by assessing the sharpness values after each acquisition as a function of depth. Each derived curve peaks around the receive focus and the unique position of the scatterer is identified by combining the data from all curves using a maximum likelihood algorithm with a calibration standard. <italic>Results:</italic> Simulated and experimental ultrasound point scatter data show that the sharpness method can provide scatterer axial localization with an average accuracy down to 10.21 <inline-formula><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula>m ( <inline-formula><tex-math notation="LaTeX">$\approx\lambda /$</tex-math></inline-formula>21) and with up to 11.4 times increased precision compared to conventional localization. The improvements depend on the rate of change of sharpness using each focus, and the signal to noise ratio in each image. <italic>Conclusion:</italic> Super-resolution axial imaging from optical microscopy has been successfully translated into ultrasound imaging by using raw ultrasound data and standard beamforming. <italic>Significance:</italic> The normalized sharpness method has the potential to be used in scatterer localization applications and contribute in current super-resolution ultrasound imaging techniques.
Quality of Extracted Sequential Rules by Session Identification Using STT and Cookies

The data source of web usage mining is a web server access log file. This paper is focus on the user session identification that is the important step of data pre-processing. There are two useful methods to identification user and session: Session Time Thresholds (STT) and cookies identification. We identified user/session with cookies and STT methods and create different data pre-processing files. We will compare the user/session identification according to following levels of data pre-processing. By comparing these methods, we focused on the quality of extracted sequential rules. Sequence rules are an important output of the web usage mining process. Generated sequential rules from pre-processed files are classified into one of the following groups: useful, trivial, inexplicable. The aim of our paper is to compare the user/session identification using cookies with the identification of user/session using the STT. This comparison was performed with respect to the quality of the sequential rules generated, i.e., a comparison was made in terms of generation useful, trivial and inexplicable rules.
A Highly Accurate Current LED Lamp Driver With Removal of Low-Frequency Flicker Using Average Current Control Method

This paper presents an average current control method for a light-emitting diode (LED) lamp driver that achieves a highly accurate current and removes low-frequency light flicker. The proposed LED lamp driver accurately maintains an average LED forward current by precisely adjusting the duration of the on- and off-times of the LED lamp driver. It also removes the low-frequency flicker by regulating the LED forward current without being affected by the low-frequency component of the ac line voltage. In addition, it reduces power consumption by eliminating the necessity of a high-voltage sensor or a high-side resistor, which causes conduction loss. The proposed average current controller was fabricated using a 0.18 μm bipolar, complementary metal-oxide-semiconductor, and double diffused metal-oxide-semiconductor process technology. The measurement results of the proposed LED lamp driver show that the variation in the average LED forward current is less than 0.6%, and the light flicker below 120 Hz is completely removed. In addition, the measured maximum power efficiency and power factor of the proposed LED lamp driver are 89.22% and 0.93, respectively.
Will the Big Data Strategic Alliance be Workable for Intelligent Vehicles and New Energy Vehicles Industry?—Perspective of System Dynamics

Different from papers on the big data technique, in this paper has study on industry-university-research big data strategic alliance stability from a system dynamics perspective. By feedback of industry-university-research big data strategic alliance stability, the causal loop diagrams of material, information and energy are analyzed from three aspects, which are aspects of matching, interactivity and all-win. Furthermore, a flow chart and system dynamics model are established to have am empirical analysis. Vensim PLE is used to simulate and test the validation and application value of model. The simulation results show that it should pay attention to role and impact of single variable in the module, and the combination and interaction between multiple module and the elements in alliance system framework for a specific alliance system to finally achieve alliance stability. So we can't only focus on the technique of big data, but also pay more attention to the process reengineering.
Traffic Planning for Time-Sensitive Communication

Many industries, including the automotive industry and industrial automation, have a need for reliable real-time communication. To satisfy this need, industry-specific, often proprietary, solutions have been developed in recent decades. Time-sensitive networking (TSN) is addressing a grand unification of these existing technologies to leverage cross-industry cost efficiency as well as to guarantee a stable growth path of communication capabilities. While the functionality of time-sensitive networking is exhaustively standardized in IEEE 802.1, configuration standards for TSN are largely missing. Thus, in this article we review the IEEE TSN standards, in particular 802.1Qbv, and continue to illustrate a reference model for traffic planning for time-sensitive communication. Furthermore, the article references a detailed technical report describing the complete model, which is ideally suited as a starting point for standardization and ensures the interoperability of future TSN traffic planning tools.
Clinical significance of repeat rebiopsy in detecting the EGFR T790M secondary mutation in patients with non-small cell lung cancer

Background Osimertinib is an essential drug to treat non-small-cell lung cancer (NSCLC) harboring the epidermal growth factor receptor (EGFR) T790M mutation, and rebiopsy is necessary to detect this mutation. However, the significance of repeat rebiopsy in NSCLC patients whose first rebiopsy was T790M-negative remains unclear. We used a retrospective cohort to clarify this issue. Methods We reviewed the medical records of patients with NSCLC harboring EGFR mutations who underwent EGFR tyrosine kinase inhibitor (TKI) treatment at Okayama University Hospital between January 2015 and January 2017. Results Of 102 patients with EGFR-mutant NSCLC, 55 underwent rebiopsy after acquired resistance to prior EGFR TKIs. Pre-existing activating EGFR mutations were found in all 55 rebiopsied samples. Of the 55 samples, 25 were T790M-positive (45%). Among the remaining 30 patients (T790M-negative on the first rebiopsy), 21 underwent additional rebiopsies following interval therapy. Of the 21 patients, 11 were T790M-positive on the second rebiopsy and 1 on the third. We also evaluated the efficacy of osimertinib in patients who needed a repeat rebiopsy to detect the T790M mutation. Osimertinib showed good activity with an objective response rate of 50%. Conclusions Repeat rebiopsy increases the ability to detect a secondary mutation (T790M) in EGFR.
Ditto Subsystem : A Case Study for Building Experiment Environment in StarBED Using TopDL

Testbed management tool is developed for the purpose of supporting user’s experiments. On the other hand, there are researches that developed a tool to enable experiments that testbed does not targeted. Although there are requests from users for using these tools, many are not provided to users in Testbed. Therefore, it is necessary to provide a framework for users to easily use or implement such tools in Testbed. We aimed to make it possible to use new tools easily without modifying of conventional Testbed management tool by implementing subsystem on testbed. In this paper, we describe the result of a case study for building the environment on StarBED resources using TopDL description which is the topology description language proposed by DeterLab.