Miracle-dz/UniFAR-FTUs huggingface dataset:
Decreasing incidence of subarachnoid hemorrhage

Objective To determine the incidence and trends in subarachnoid hemorrhage in Ireland using data from a national database. Materials and methods We performed a retrospective nationwide query of the Irish Hospital In-patient Enquiry System (HIPE). This is a national database of all in-patient activity in acute public hospitals in Ireland. Each HIPE entry records one episode of in-patient care. The study period ranged from 1997 to 2015. Population data was obtained from the Irish Central Statistics Office, and the annual prevalence of smoking from the Irish National Tobacco Control Office. We were therefore able to calculate both crude annual acute subarachnoid hemorrhage (SAH) incidence rates, as well as population-standardized rates, and compared them with trends in the annual smoking rates. Results The mean number of SAH cases per year is 549, with 465 cases in 1997 and 517 in 2015 (range: 465–624). The absolute incidence of SAH, therefore, remained relatively stable. Due to population increases over time, the population-adjusted rate of SAH therefore decreased, from 126.9/million people/year in 1997 to 111.5/million people/year in 2015. Nationally, there was a decrease in smoking prevalence, from 31% in 1998 to 19.2% in 2015. There was a statistically significant correlation between decreasing smoking rates and decreasing population-adjusted incidence of SAH (P=<0.0001). Conclusions Our data suggests that the incidence of non-traumatic subarachnoid hemorrhage in our population appears to be decreasing, a decrease which is correlated with decreasing smoking rates. This provides important data both in terms of the epidemiology of SAH, as well as the possible role of public-health interventions in tackling both smoking and declining rates of SAH.
Importance of Normalization of CA19-9 Levels Following Neoadjuvant Therapy in Patients With Localized Pancreatic Cancer.

OBJECTIVE Carbohydrate antigen 19-9 (CA19-9) is a prognostic marker for patients with pancreatic cancer (PC), but its value as a treatment biomarker is unclear. SUMMARY BACKGROUND DATA Although CA19-9 is an established prognostic marker for patients with PC, it is unclear how CA19-9 monitoring should be used to guide multimodality treatment and what level of change in CA19-9 constitutes a meaningful treatment response. METHODS CA19-9 measurements at diagnosis (pretx), after completion of all planned neoadjuvant therapy (preop), and after surgery (postop) were analyzed in patients with localized PC who had an elevated CA19-9 (≥35 U/dL) at diagnosis. Patients were classified by: 1) quartiles of pretx CA19-9 (Q1-4); 2) proportional changes in CA19-9 (ΔCA19-9) after the completion of neoadjuvant therapy; 3) normalization (CA19-9 <35 U/dL) of preop CA19-9; and 4) normalization of postop CA19-9. RESULTS Among 131 patients, the median overall survival (OS) was 30 months; 68 months for the 33 patients in Q1 of pretx CA19-9 (<80 U/dL) compared with 25 months for the 98 patients in Q2-4 (P = 0.03). For the 98 patients in Q2-4, preop CA19-9 declined (from pretx) in 86 (88%), but there was no association between the magnitude of ΔCA19-9 and OS (P = 0.77). Median OS of the 98 patients who did (n = 29) or did not (n = 69) normalize their preop CA19-9 were 46 and 23 months, respectively (P = 0.02). Of the 69 patients with an elevated preop CA19-9, 32 (46%) normalized their postop CA19-9. Failure to normalize preop or postop CA19-9 was associated with a 2.77-fold and 4.03-fold increased risk of death, respectively (P < 0.003) as compared with patients with normal preop CA19-9. CONCLUSIONS Following neoadjuvant therapy, normalization of CA19-9, rather than the magnitude of change, is the strongest prognostic marker for long-term survival.
Morphological revision of the Subgroup 1 Fauchald, 1970 of Marphysa de Quatrefages, 1865 (Eunicidae: Polychaeta).

Fifteen species of Marphysa classified in the Subgroup 1 Fauchald (1970) were reviewed and evaluated in a morphological analysis of the subgroup. It was found that 13 of these have a characteristic morphological pattern distinct from that of Marphysa sensu stricto; as a consequence, a new genus is proposed, Paucibranchia n. gen. This new genus includes the species that have branchiae restricted to a few chaetigers in the anterior region, maxillae I with a rounded falcal arch and outer edge with a straight base plus a curvature in the basal inner edge, dorsal cirri longer in the branchial region and in media-posterior region as long or longer than pre-branchial chaetigers, and the postchaetal lobe in the branchial region well developed, elongated. Paucibranchia n. gen. includes six new species (P. andresi n. sp., P. carrerai n. sp., P. gathofi n. sp., P. gilberti n. sp., P. miroi n. sp. and P. patriciae n. sp.), two species not formally named, and other 13 species previously included in Marphysa (P. adenensis (Gravier, 1900) n. comb. , P. bellii (Audouin Milne-Edwards, 1833) n. comb. , P. cinari (Kurt-Sahin, 2014) n. comb. , P. conferta (Moore, 1911) n. comb. , P. disjuncta (Hartman, 1961) n. comb. , P. fallax (Marion Bobretzky, 1875) n. comb. , P. gemmata (Mohammad, 1973) n. comb. , P. kinbergi (McIntosh, 1910) n. comb. , P. oculata (Treadwell, 1921) n. comb. , P. purcellana (Willey, 1904) n. comb. , P. sinensis (Monro, 1934) n. comb. , P. stragula (Grube, 1878) n. comb. , P. totospinata (Lu Fauchald, 1998) n. comb. ). One species previously classified in the subgroup, Marphysa striata (Kinberg, 1865), was considered indeterminate. Finally, some statistical analyses on size dependent features and an identification key for species of the new genus were included.
Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis

Herbicide-resistance traits are the most widely used agriculture biotechnology products. Yet, to maintain their effectiveness and to mitigate selection of herbicide-resistant weeds, the discovery of new resistance traits that use different chemical modes of action is essential. In plants, the Gretchen Hagen 3 (GH3) acyl acid amido synthetases catalyze the conjugation of amino acids to jasmonate and auxin phytohormones. This reaction chemistry has not been explored as a possible approach for herbicide modification and inactivation. Here, we examined a set of Arabidopsis GH3 proteins that use the auxins indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) as substrates along with the corresponding auxinic phenoxyalkanoic acid herbicides 2,4-dichlorophenoxylacetic acid (2,4-D) and 4-(2,4-dichlorophenoxy)butyric acid (2,4-DB). The IBA-specific AtGH3.15 protein displayed high catalytic activity with 2,4-DB, which was comparable to its activity with IBA. Screening of phenoxyalkanoic and phenylalkyl acids indicated that side-chain length of alkanoic and alkyl acids is a key feature of AtGH3.15's substrate preference. The X-ray crystal structure of the AtGH3.15·2,4-DB complex revealed how the herbicide binds in the active site. In root elongation assays, Arabidopsis AtGH3.15-knockout and -overexpression lines grown in the presence of 2,4-DB exhibited hypersensitivity and tolerance, respectively, indicating that the AtGH3.15-catalyzed modification inactivates 2,4-DB. These findings suggest a potential use for AtGH3.15, and perhaps other GH3 proteins, as herbicide-modifying enzymes that employ a mode of action different from those of currently available herbicide-resistance traits.
Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis.

The helicase-primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase-primase interaction in M. tuberculosis, a complex was modeled using the MtDnaG-CTD and MtDnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of MtDnaG were identified as potential key residues interacting with MtDnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of MtDnaB-NTD with the Ile605Ala mutant of MtDnaG-CTD compared with native MtDnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB-DnaG complex. Also, MtDnaB-NTD showed micromolar affinity with DnaG-CTDs from Escherichia coli and Helicobacter pylori and unstable binding with DnaG-CTD from Vibrio cholerae The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.
Chitosan Hydrogel Beads Functionalized with Thymol-Loaded Solid Lipid–Polymer Hybrid Nanoparticles

In this study, the innovative and multifunctional nanoparticles–hydrogel nanocomposites made with chitosan hydrogel beads and solid lipid–polymer hybrid nanoparticles (SLPN) were prepared through conjugation between SLPN and chitosan beads. The SLPNs were first fabricated via coating the bovine serum albumin (BSA)-emulsified solid lipid nanoparticles with oxidized dextran. The aldehyde groups of the oxidized dextran on the surface of the SLPN enabled an in situ conjugation with the chitosan beads through the Schiff base linkage. The obtained nano-on-beads composite exhibited a spherical shape with a homogeneous size distribution. The successful conjugation of SLPN on the chitosan beads was confirmed by a Fourier transform infrared spectroscopy and a scanning electron microscope. The effects of the beads dosage (50, 100, 200, and 300 beads) and the incubation duration (30, 60, 90, 120, and 150 min) on the conjugation efficiency of SLPN onto the beads were comprehensively optimized. The optimal formulations were found to be a 200 bead dosage, with 30–90 min incubation duration groups. The optimal formulations were then used to encapsulate thymol, an antibacterial agent, which was studied as a model compound. After encapsulation, the thymol exhibited sustained release profiles in the phosphate buffer saline. The as-prepared nanoparticles–hydrogel nanocomposites reported in this proof-of-concept study hold promising features as a controlled-release antibacterial approach for improving food safety.
Reduction of response time by data placement reflecting co-occurrence structures in structured overlay networks

We propose a method to accelerate a response of structured overlay networks by reducing the number of hops required to answer multi-queries. In the proposed method, by copying data items to the redundant storage spaces in other storages, a good data placement reflecting co-occurrence structures in the structured overlay network is achieved. We formulate the optimization problem of the data placement in the limited redundant space of the storages as an integer programming. A greedy approach to solve the optimization problem is also proposed. Through several simulations, it is confirmed that the proposed method can reduce the average number of hops required to answer multi-queries by about 30% at the maximum in our simulation settings. The reduction rate of the average number of hops depends on the level of co-occurrence. Further, the reduction of the computation time to solve the optimization problem with the greedy approach is evaluated. We also confirm that the proposed method does not affect load balancing of structured overlay networks.
Reverse pneumatic artificial muscles (rPAMs): Modeling, integration, and control

Despite offering many advantages over traditional rigid actuators, soft pneumatic actuators suffer from a lack of comprehensive, computationally efficient models and precise embedded control schemes without bulky flow-control valves and extensive computer hardware. In this article, we consider an inexpensive and reliable soft linear actuator, called the reverse pneumatic artificial muscle (rPAM), which consists of silicone rubber that is radially constrained by symmetrical double-helix threading. We describe analytical and numerical static models of this actuator, and compare their performance against experimental results. To study the application of rPAMs to operate underlying kinematic linkage skeletons, we consider a single degree-of-freedom revolute joint that is driven antagonistically by two of these actuators. An analytical model is then derived, and its accuracy in predicting the static joint angle as a function of input pressures is presented. Using this analytical model, we perform dynamic characterization of this system. Finally, we propose a sliding-mode controller, and a sliding mode controller augmented by a feed-forward term to modulate miniature solenoid valves that control air flow to each actuator. Experiments show that both controllers function well, while the feed-forward term improves the performance of the controller following dynamic trajectories.
Security of Separated Data in Cloud Systems with Competing Attack Detection and Data Theft Processes

Empowered by virtualization technology, service requests from cloud users can be honored through creating and running virtual machines. Virtual machines established for different users may be allocated to the same physical server, making the cloud vulnerable to co‐residence attacks where a malicious attacker can steal a user's data through co‐residing their virtual machines on the same server. For protecting data against the theft, the data partition technique is applied to divide the user's data into multiple blocks with each being handled by a separate virtual machine. Moreover, early warning agents (EWAs) are deployed to possibly detect and prevent co‐residence attacks at a nascent stage. This article models and analyzes the attack success probability (complement of data security) in cloud systems subject to competing attack detection process (by EWAs) and data theft process (by co‐residence attackers). Based on the suggested probabilistic model, the optimal data partition and protection policy is determined with the objective of minimizing the user's cost subject to providing a desired level of data security. Examples are presented to illustrate effects of different model parameters (attack rate, number of cloud servers, number of data blocks, attack detection time, and data theft time distribution parameters) on the attack success probability and optimization solutions.
Identification of the Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer

Background: Patients with locally advanced or recurrent prostate cancer typically undergo androgen deprivation therapy (ADT), but the benefits are often short-lived and the responses variable. ADT failure results in castration-resistant prostate cancer (CRPC), which inevitably leads to metastasis. We hypothesized that differences in tumor transcriptional programs may reflect differential responses to ADT and subsequent metastasis. Results: We performed whole transcriptome analysis of 20 patient-matched Pre-ADT biopsies and 20 Post-ADT prostatectomy specimens, and identified two subgroups of patients (high impact and low impact groups) that exhibited distinct transcriptional changes in response to ADT. We found that all patients lost the AR-dependent subtype (PCS2) transcriptional signatures. The high impact group maintained the more aggressive subtype (PCS1) signal, while the low impact group more resembled an AR-suppressed (PCS3) subtype. Computational analyses identified transcription factor coordinated groups (TFCGs) enriched in the high impact group network. Leveraging a large public dataset of over 800 metastatic and primary samples, we identified 33 TFCGs in common between the high impact group and metastatic lesions, including SOX4/FOXA2/GATA4, and a TFCG containing JUN, JUNB, JUND, FOS, FOSB, and FOSL1. The majority of metastatic TFCGs were subsets of larger TFCGs in the high impact group network, suggesting a refinement of critical TFCGs in prostate cancer progression. Conclusions: We have identified TFCGs associated with pronounced initial transcriptional response to ADT, aggressive signatures, and metastasis. Our findings suggest multiple new hypotheses that could lead to novel combination therapies to prevent the development of CRPC following ADT.
A Gradient-based Approach to a class of Hybrid Optimal control Problems

Abstract We investigate optimal control problems for a class of non-stationary hybrid systems with autonomous location transitions. Using the Lagrange approach and the technique of the reduced gradient, we derive necessary optimality conditions for the considered class of problems. These optimality conditions are closely related to a variant of the Hybrid Maximum Principle and can be used for constructive optimization algorithms.
Early career experiences of navigating journal article publication: Lessons learned using an autoethnographic approach

The successful publication of peer reviewed academic journal articles is an essential achievement for early career researchers (ECRs) seeking to establish themselves in their profession. However, this journey can pose several significant challenges for ECRs. We use an autoethnographic approach that draws deeply on our lived experience as ECRs to capture our recent and current experiences of negotiating the academic journal article publication journey to explore the tensions, contradictions, and benefits encountered in the journey. We critically examine challenges we experienced in choosing a target journal and negotiating the follow‐up process; undertaking revisions; and our experiences of limitations and possibilities in peer review and editorial support. While the peer review journal writing process has played a significant role in supporting us to become more effective ECRs, we also highlight challenges we faced negotiating ethical quandaries in this space, as well as illustrate how our preconceptions of a simple publication journey were confounded by subsequent experience of the complex realities of the space. We also suggest that educational interventions are indicated to provide ECRs support in foundational knowledge about what constitutes valuable revisions, an effective paper, and the scope of issues that can be addressed to make a paper more effective, with reference to the possibility of academic mentoring to support this need. Finally, we explore our findings in light of the tensions imposed by the relative inexperience and lack of power yielded by ECRs.
Craniodental Allometry, Prenatal Growth Rates, and the Evolutionary Loss of the Third Molars in New World Monkeys

A growing body of literature demonstrates that genetic patterning mechanisms underlie the relative proportions of the mammalian postcanine dentition with the third molar being key to understanding variation within the molar row. With this relatively recent insight, there has been renewed interest in mammalian taxa that have lost the third molars. Within platyrrhines, the marmosets and tamarins (Callitrichidae family) are characterized by small body size, claw‐like nails, twinning, and reduced molar number. Small body size is hypothesized to have resulted in the third molar being crowded out of the jaws leading to its evolutionary loss in this family. To further explore this hypothesis, we measured the cranium and dentition of 142 individuals spanning all five platyrrhine families. These data reveal that callitrichids have a significantly smaller proportion of mandibular postcanine tooth row length relative to other platyrrhines, refuting the “crowding out” hypothesis. However, postcanine tooth row length is significantly correlated with mandibular length and cranial length (P < 0.01) across all platyrrhines providing evidence for a strong allometric association between postcanine tooth row length and body size more generally. The small body size that characterizes callitrichids results in part from slower prenatal growth rates. Given the allometric relationship between postcanine tooth row length and body size, reported here and in previous studies, we hypothesize that the evolutionary loss of the third molars in callitrichids results from the inhibition of third molar development as a consequence of the slower prenatal growth rates associated with small body size in this family. Anat Rec, 302:1419–1433, 2019. © 2018 Wiley Periodicals, Inc.
Modelling and forecasting of signal-to-interference plus noise ratio in femtocellular networks using logistic smooth threshold autoregressive model

The aim of this paper is to present a non-linear statistical model to fit and forecast the signal-to-interference plus noise ratio (SINR) in two-tier heterogeneous cellular networks which consist of macrocells and femtocells. Since in these networks the number and locations of femtocell base stations (FBS) are variable, SINR forecasting can be useful in some areas such as power control and handover management. So far, linear autoregressive (AR) models have commonly been used in forecasting the received signal strength (rss) in macrocellular networks. However, AR modelling results in high mean square error (MSE) when data are non-linear. This paper focuses on SINR which takes into account signal strength, interference and noise effects. Moreover, macro-femto cellular network is considered. The F-test results show that the SINR data are non-linear, leading to use non-linear models instead of AR model. A non-linear logistic smooth threshold AR (LSTAR) model is utilised to model and forecast the SINR data. Kolmogorov–Smirnov (K-S) test demonstrates that LSTAR provides good fitness to the SINR samples. The results indicate that LSTAR model achieves much better performance in modelling and forecasting of SINR data than the AR model.
What PD Research in China Tells Us

Peritoneal dialysis (PD) was introduced in China later than in most Western countries, and PD research activity was quite limited until the 1990s. However, in the 2000s, and even more so during the last decade, there has been an unsurpassed increase in the number of PD patients, paralleled by a substantial increase in PD research activity reflected by an increasing number of PD papers from China. In this brief review, we describe some of the factors that may explain the dramatic developments in PD research in mainland China, such as the focus on basic research using scientific approaches that subsequently could be applied also in clinical studies. Another important factor was the growing interactions with international PD research centers in Hong Kong and in Western countries. Thanks to strong support from Chinese national and regional funding sources, a growing number of young Chinese researchers went to key international PD centers to learn about novel advanced research techniques. This paved the way for long-lasting, productive collaborations with benefits also for the foreign host institutions. Finally, we present some current research projects, including basic research that may contribute to the understanding of mechanisms behind complications such as peritonitis, and clinical projects aiming at improving PD management guidelines and better understanding of the potential of PD in China. Because of the size of the PD population, now the largest in the world, and the increasing number, and quality, of researchers in the PD field, PD research in China is destined to be a major contributor to advancements in PD in the near future.