Miracle-dz/UniFAR-FTUs huggingface dataset:
Chondrosarcoma of the Osseous Spine Treated by Surgery With or Without Radiotherapy: A Propensity Score Matched and Grade/Stage-stratified Study

Study Design: This was a longitudinal cohort study. Objective: The main objective of this study was to investigate the outcomes of surgery with or without radiotherapy during treatment of patients with chondrosarcoma of the osseous spine. Summary of Background Data: Chondrosarcoma is a primary spinal malignant tumor; chemotherapy and radiotherapy (RT) are generally unsuccessful, and thus, the main treatment of choice is complete en bloc resection. However, even with complete resection, these patients still have a significant rate of recurrence, morbidity, and mortality. Although there have been reports that the addition of RT to surgery may lead to increased survival and better cancer control, the evidence of the efficacy of RT remains controversial. Materials and Methods: Patients diagnosed with chondrosarcoma who are then treated by surgery alone or surgery+RT were identified and extracted from the SEER (Surveillance, Epidemiology, and End Results) database (1973-2013). Propensity score matched (PSM) analysis was performed to balance patient characteristics between surgery alone and surgery+RT groups. Patients with a different grade and stage were stratified and analyzed. Results: A total of 778 patients with chondrosarcoma of the osseous spine treated by surgery alone or surgery+RT were extracted from the SEER database. Before PSM, the unadjusted Kaplan-Meier curve and bivariable Cox proportional hazard regression models showed that the surgery alone group had higher chondrosarcoma cancer–specific survival and overall survival than the surgery+RT group (both P<0.001), while the difference was attenuated after PSM. Stratified analysis found that RT was worse for low-grade chondrosarcoma patients and had a better trend for high-grade chondrosarcoma patients. Conclusions: The results of our present study suggest that low-grade chondrosarcoma of the osseous spine is resistant to RT, while high-grade chondrosarcoma patients had a better trend with RT. Level of Evidence: Level III.
Pushing intelligence to the network edge

Networking has already entered a new era where it is evolving into the Internet of Things (IoT). The future network consists of tens of billions of connected devices. These things bear different security vulnerabilities and can be abused to perform diverse attacks. Due to the heterogeneous nature of IoT and its massive deployment, managing the IoT security requires automated techniques to deal with the emerging security challenges. To address this problem, we propose a model where intelligence is integrated at the network edge to extract specific statistical features per network flow. These features are passed to a controller which implements a classification algorithm to determine the device type generating the observed flow. A monitoring module is responsible for analyzing the network traffic behavior. If abnormal traffic is detected from a certain device, the controller takes the adequate action (e.g. blocking the traffic from this device). After collecting data from IoT devices, we evaluate our proposed classification model. Results show that our approach can achieve up to 99.6% accuracy for device type identification and up to 99.9% for traffic type classification.
Genetic Diversity and Drug Susceptibility of Mycobacterium tuberculosis Isolates in a Remote Mountain Area of China.

OBJECTIVE We determined the genetic diversity of Mycobacterium tuberculosis (MTB) in a remote mountainous area of southwest China and evaluated the resolving ability of single nucleotide polymorphism (SNP) genotyping combined with variable number tandem repeat (VNTR) genotyping for Beijing family strains in association with drug resistance status. METHODS Three hundred thirty-one MTB strains were isolated from patients living in mountainous regions of southwest China, and 8-loci SNP, VNTR-15 genotyping assays, and drug susceptibility testing of 9 drugs were performed. RESULTS A total of 183 [55.29% (183/331)] strains were classified into the Beijing family. Of the 183 strains, 111 (60.66%) were defined as modern Beijing strains. The most predominant modern Beijing sub-lineage and ancient Beijing sub-lineage were Bmyc10 [39.34% (72/183)] and Bmyc25 [20.77% (38/183)], respectively. Of the isolates, 19.64% (65/331) were resistant to at least 1 of the 9 anti-TB drugs and 17 [4.98% (17/331)] MTB isolates were multi-drug resistant tuberculosis (MDR-TB). Two hundred sixty-one isolates showed a clustering rate of 14.18% (37/261) and a discriminatory index of 0.9990. The Beijing lineage exhibited a significantly higher prevalence of MDR-TB, as well as resistance to isoniazid (INH), rifampin (RIF), and para-aminosalicylic acid (PAS) when analyzed independently (P = 0.005, P = 0.017, P = 0.014, and P = 0.006 respectively). The Beijing lineage was not associated with genetic clustering or resistance to any drug. In addition, genetic clustering was not associated with drug resistance. CONCLUSION MTB strains demonstrate high genetic diversity in remote mountainous areas of southwest China. Beijing strains, especially modern Beijing strains, are predominant in remote mountainous area of China. The combination of 8-loci SNPs and VNTR-15 genotyping is a useful tool to study the molecular epidemiology of MTB strains in this area.
Development of caudal structures of a morphogenetic mutant (Da) in the teleost fish, medaka (Oryzias latipes)

Development of the internal structures of the caudal region (muscles, bones, cartilages, nerves, and blood vessels) of the Da/Da mutant medaka and of wild‐type +/+ fish was compared. Muscles and nerves were immunochemically stained by using an antibody to troponin T and antibodies to neurofilament proteins, respectively. Bones and cartilages were stained with alizarin red and alcian blue. In stages 31–32 of the Da/Da embryo, the rudiments of epurals 1, 2, and 3 differentiated dorsally opposite the sites of the ventral rudiments of the parhypural, the lower hypural plate, and the upper hypural plate, respectively. In the +/+ embryo, the rudiments of epurals 1 and 2 differentiated in the later developmental stages (after stage 34), but the rudiment of epural 3 did not differentiate. In the Da/Da embryo, the deep dorsal flexor passed dorsalwards and ended at the rudiment of epural 2, whereas the muscle passed ventralwards and ended at the rudiment of the upper hypural plate in the +/+ embryo. In the Da/Da fry, the epichordal region of the caudal fin fold grew and the notochord extended straight into the tail without bending, while in the + /+ fry, the epichordal region did not grow and the notochord turned dorsalwards within the tail. In the Da/Da fry, extra skeletal rudiments and musculature differentiated in the epichordal region of the caudal fin, whereas these supernumerary structures did not develop in the +/+ fry. The pattern of the epichordal skeleton and musculature in the caudal region of the adult Da/Da fish was an almost mirror‐image duplication of the hypochordal structures. These observations suggest that the characteristic expansion of the dorsal fin and epichordal lobe in the caudal region of the adult Da/Da fish is due to a process of ventralization, whereby the dorsal skeleton, musculature, and fin fold are stimulated to differentiate in a pattern like that which is restricted to the anal fin and hypochordal lobe of the wild type.
How much randomization is needed to deter collaborative cheating on asynchronous exams?

This paper investigates randomization on asynchronous exams as a defense against collaborative cheating. Asynchronous exams are those for which students take the exam at different times, potentially across a multi-day exam period. Collaborative cheating occurs when one student (the information producer) takes the exam early and passes information about the exam to other students (the information consumers) that are taking the exam later. Using a dataset of computerized exam and homework problems in a single course with 425 students, we identified 5.5% of students (on average) as information consumers by their disproportionate studying of problems that were on the exam. These information consumers ("cheaters") had a significant advantage (13 percentage points on average) when every student was given the same exam problem (even when the parameters are randomized for each student), but that advantage dropped to almost negligible levels (2--3 percentage points) when students were given a random problem from a pool of two or four problems. We conclude that randomization with pools of four (or even three) problems, which also contain randomized parameters, is an effective mitigation for collaborative cheating. Our analysis suggests that this mitigation is in part explained by cheating students having less complete information about larger pools.
NLP-assisted software testing: a systematic review

Context: To reduce manual effort of extracting test cases from natural-language requirements, many approaches based on Natural Language Processing (NLP) have been proposed in the literature. Given the large number of approaches in this area, and since many practitioners are eager to utilize such techniques, it is important to synthesize and provide an overview of the state-of-the-art in this area. Objective: Our objective is to summarize the state-of-the-art in NLP-assisted software testing which could benefit practitioners to potentially utilize those NLP-based techniques, benefit researchers in providing an overview of the research landscape. Method: To address the above need, we conducted a survey in the form of a systematic literature mapping (classification) and systematic literature review. After compiling an initial pool of 57 papers, we conducted a systematic voting, and our final pool included 50 technical papers. Results: This review paper provides an overview of contribution types in the papers, types of NLP approaches used to assist software testing, types of required input requirements, and a review of tool support in this area. Among our results are the followings: (1) only 2 of the 28 tools (7%) presented in the papers are available for download; (2) a larger ratio of the papers (23 of 50) provided a shallow exposure to the NLP aspects (almost no details). Conclusion: We believe that this paper would benefit both practitioners and researchers by serving as an "index" to the body of knowledge in this area. The results could help practitioners by enabling them to utilize any of the existing NLP-based techniques to reduce cost of test-case design and decrease the amount of human resources spent on test activities. Initial insights, after sharing this review with some of our industrial collaborators, show that this review can indeed be useful and beneficial to practitioners.
Identification and Characterization of Neuropeptides by Transcriptome and Proteome Analyses in a Bivalve Mollusc Patinopecten yessoensis

Neuropeptides play essential roles in regulation of reproduction and growth in marine molluscs. But their function in marine bivalves – a group of animals of commercial importance – is largely unexplored due to the lack of systematic identification of these molecules. In this study, we sequenced and analyzed the transcriptome of nerve ganglia of Yesso scallop Patinopecten yessoensis, from which 63 neuropeptide genes were identified based on BLAST and de novo prediction approaches, and 31 were confirmed by proteomic analysis using the liquid chromatography-tandem mass spectrometry (LC-MS/MS). Fifty genes encode known neuropeptide precursors, of which 20 commonly exist in bilaterians and 30 are protostome specific. Three neuropeptides that have not yet been reported in bivalves were identified, including calcitonin/DH31, lymnokinin and pleurin. Characterization of glycoprotein hormones, insulin-like peptides, allatostatins, RFamides, and some reproduction, cardioactivity or feeding related neuropeptides reveals scallop neuropeptides have conserved molluscan neuropeptide domains, but some (e.g., GPB5, APGWamide and ELH) are characterized with bivalve-specific features. Thirteen potentially novel neuropeptides were identified, including 10 that may also exist in other protostomes, and 3 (GNamide, LRYamide, and Vamide) that may be scallop specific. In addition, we found neuropeptides potentially related to scallop shell growth and eye functioning. This study represents the first comprehensive identification of neuropeptides in scallop, and would contribute to a complete understanding on the roles of various neuropeptides in endocrine regulation in bivalve molluscs.
Neuromuscular organization and regional EMG activity of the pectoralis in the pigeon

In order to improve our understanding of the neuromuscular control of the most massive avian flight muscle, we studied the innervation pattern of the pigeon pectoralis. Nine primary branches from the rostral trunk and nine to ten branches from the caudal trunk of the pectoral nerve were identified by microdissection in ten pigeons. The region of muscle that each branch innervates was delineated by nerve stimulation studies (ten pigeons) and six regions were confirmed by glycogen depletion (ten pigeons). In pigeons, branches from the rostral nerve innervate the anterior 3/5 of the sternobrachialis (SB) head of the pectoralis and branches from the caudal trunk innervate the posterior 1/2 of the SB and all of the throacobrachials (TB). In the SB, individual branches of the rostral pectoral nerve innervate wedge‐shaped muscle regions (each approximately 1.3 cm wide), collectively forming a fan shaped arrangement along the sternal carina. Adjacent muscle regions partially overlap at their boundaries. Within the thoracobrachialis (TB) head of the pectrolis, muscle regions are wider. There is a region in mid‐SB‐where the innervation territories of the rostral and caudal nerves oferlap. Electromyographic (EMG) activity patterns were recorded within ten of the identified muscle regions during take‐off, level flapping flight, and landing. Onset of EMG activity and EMG intensity within various muscle regions exhibits significant differences both within a wingbeat cycle and among different modes of flight. The innervation pattern of the pectoralis presents the anatomical substrate for neuromuscular compartmentalization and differential EMG activity within the pectoralis may reflect sensory‐motor partitioning. The extent to which the neuromuscular compartmentalization of the pectoralis corresponds to its ability to produce an array of force vectors to the wing awaits further more detailed biomechanical studies. © 1993 Wiley‐Liss, Inc.
Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection

Laboratory models are often used to understand the interaction of related pathogens via host immunity. For example, recent experiments where ferrets were exposed to two influenza strains within a short period of time have shown how the effects of cross-immunity vary with the time between exposures and the specific strains used. On the other hand, studies of the workings of different arms of the immune response, and their relative importance, typically use experiments involving a single infection. However, inferring the relative importance of different immune components from this type of data is challenging. Using simulations and mathematical modelling, here we investigate whether the sequential infection experiment design can be used not only to determine immune components contributing to cross-protection, but also to gain insight into the immune response during a single infection. We show that virological data from sequential infection experiments can be used to accurately extract the timing and extent of cross-protection. Moreover, the broad immune components responsible for such cross-protection can be determined. Such data can also be used to infer the timing and strength of some immune components in controlling a primary infection, even in the absence of serological data. By contrast, single infection data cannot be used to reliably recover this information. Hence, sequential infection data enhances our understanding of the mechanisms underlying the control and resolution of infection, and generates new insight into how previous exposure influences the time course of a subsequent infection.
Universal statistics of Fisher information in deep neural networks: mean field approach

The Fisher information matrix (FIM) is a fundamental quantity to represent the characteristics of a stochastic model, including deep neural networks (DNNs). The present study reveals novel statistics of FIM that are universal among a wide class of DNNs. To this end, we use random weights and large width limits, which enables us to utilize mean field theories. We investigate the asymptotic statistics of the FIM’s eigenvalues and reveal that most of them are close to zero while the maximum eigenvalue takes a huge value. Because the landscape of the parameter space is defined by the FIM, it is locally flat in most dimensions, but strongly distorted in others. Moreover, we demonstrate the potential usage of the derived statistics in learning strategies. First, small eigenvalues that induce flatness can be connected to a norm-based capacity measure of generalization ability. Second, the maximum eigenvalue that induces the distortion enables us to quantitatively estimate an appropriately sized learning rate for gradient methods to converge.
Population Pharmacokinetics of UCN-01

UCN-01 (7-Hydroxystaurosporine) is an investigational anticancer agent that is currently being evaluated as targeted therapy in phase II clinical studies. The aims of this work were to describe the population pharmacokinetics of UCN-01 in patients with advanced solid tumors, and to identify covariates in patients with advanced solid tumors that affected the pharmacokinetic parameters of UCN-01. The utility of performing this research is to provide optimization of treatment and individualized dose therapy for minimization of toxicity. So, in addition to elucidating the population pharmacokinetic parameter estimates from a Phase I trial where UCN-01 was given in combination with carboplatin in patients with advanced solid tumors, and a trial where the drug was given alone as a 72-hour infusion in the same type of population, a covariate analysis was performed in order to identify pharmacokinetic determinants of UCN-01. Using NONMEM to perform nonlinear mixed-effects modeling, a linear two-compartment model was found to provide the best fit for UCN-01 data. A meta-analysis was performed, which included pooled 3-hour and 72-hour infusion data, and provided population pharmacokinetic estimates for CL (0.0157 L/hr [6.1%RSE]), V1 (2.51 L [10.0% RSE]), Q (4.05 L/hr [14.3% RSE]), and V2 (8.39 L [6.6% RSE]). Inter-individual variability was found for each of the main pharmacokinetic parameters to be ETACL (44.9% [20.8% RSE]), ETAV1 (43.9% [39.8% RSE]), ETAQ (6.09% [62.5% RSE]), and ETAV2 (4.17% [30.0% RSE]). Body surface area was found to be a statistically-significant variable from one of the individual study analyses (3-hour infusion). Population PK modeling has contributed to a better understanding of the clinical pharmacology of UCN-01. Dose individualization may improve treatment with UCN-01. Further clinical development may be supported by optimization of combination chemotherapy.
Crystalline Modification and Its Effects on Dielectric Breakdown Strength and Space Charge Behavior in Isotactic Polypropylene

Adding nucleating agents (NAs) is one of the most efficient ways to obtain improved mechanical, optical, and thermal properties of isotactic polypropylene (iPP). While it is well appreciated that electrical property is critically affected by crystalline modification, the role between them remains unclear. Here, we address this issue by incorporating commercial α-NA and β-NA into iPP, both of which exhibit strong nucleation ability, e.g., reducing the size of crystalline agglomerates from 45.3 μm (Pure-iPP) to 2.5 μm (α-iPP) and 7.6 μm (β-iPP), respectively. Mechanical testing results show that while β-modification decreases the tensile strength a little, it does enhance the elongation at break (200%) and toughness (25.3% higher), relative to its unfilled counterparts. Moreover, a well-dispersed β-iPP system obtains a comprehensive improvement of electrical properties, including dielectric breakdown strength, space charge suppression, and internal field distortion under a high external field (−100 kV/mm) due to newly-generated deep charge trapping sites. This crystalline modification strategy is attractive for future development of many engineering insulating polymers.
Complex Word Identification Based on Frequency in a Learner Corpus

We introduce the TMU systems for the Complex Word Identification (CWI) Shared Task 2018. TMU systems use random forest classifiers and regressors whose features are the number of characters, the number of words, and the frequency of target words in various corpora. Our simple systems performed best on 5 tracks out of 12 tracks. Our ablation analysis revealed the usefulness of a learner corpus for CWI task.
Turán Function and H-Decomposition Problem for Gem Graphs

Abstract Given a graph H, the Turán function ex(n,H) is the maximum number of edges in a graph on n vertices not containing H as a subgraph. For two graphs G and H, an H-decomposition of G is a partition of the edge set of G such that each part is either a single edge or forms a graph isomorphic to H. Let ϕ (n,H) be the smallest number ϕ such that any graph G of order n admits an H-decomposition with at most ϕ parts. Pikhurko and Sousa conjectured that ϕ (n,H) = ex(n,H) for χ (H) ≥ 3 and all sufficiently large n. Their conjecture has been verified by Özkahya and Person for all edge-critical graphs H. In this article, we consider the gem graphs gem4 and gem5. The graph gem4 consists of the path P4 with four vertices a, b, c, d and edges ab, bc, cd plus a universal vertex u adjacent to a, b, c, d, and the graph gem5 is similarly defined with the path P5 on five vertices. We determine the Turán functions ex(n, gem4) and ex(n, gem5), and verify the conjecture of Pikhurko and Sousa when H is the graph gem4 and gem5.