Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural bases for F plasmid conjugation and F pilus biogenesis in Escherichia coli

Significance Bacterial “sex,” or conjugation, is a central mechanism underlying the proliferation of antibiotic resistance. Despite the discovery of conjugation by F plasmids in Escherichia coli over seven decades ago, we have only now visualized the F-encoded transfer channel and F pilus-associated platforms in the E. coli cell envelope by cryoelectron tomography. The channel supports plasmid transfer or assembly of F pili, which remarkably upon synthesis are deposited onto alternative basal structures around the cell surface. The F plasmid transfer system is a paradigm for the bacterial type IV secretion system (T4SS) superfamily. Consequently, the F-encoded structures are broadly informative of mechanisms underlying the biogenesis and function of type IV secretion machines and associated conjugative pili. Bacterial conjugation systems are members of the large type IV secretion system (T4SS) superfamily. Conjugative transfer of F plasmids residing in the Enterobacteriaceae was first reported in the 1940s, yet the architecture of F plasmid-encoded transfer channel and its physical relationship with the F pilus remain unknown. We visualized F-encoded structures in the native bacterial cell envelope by in situ cryoelectron tomography (CryoET). Remarkably, F plasmids encode four distinct structures, not just the translocation channel or channel-pilus complex predicted by prevailing models. The F1 structure is composed of distinct outer and inner membrane complexes and a connecting cylinder that together house the envelope-spanning translocation channel. The F2 structure is essentially the F1 complex with the F pilus attached at the outer membrane (OM). Remarkably, the F3 structure consists of the F pilus attached to a thin, cell envelope-spanning stalk, whereas the F4 structure consists of the pilus docked to the OM without an associated periplasmic density. The traffic ATPase TraC is configured as a hexamer of dimers at the cytoplasmic faces of the F1 and F2 structures, where it respectively regulates substrate transfer and F pilus biogenesis. Together, our findings present architectural renderings of the DNA conjugation or “mating” channel, the channel–pilus connection, and unprecedented pilus basal structures. These structural snapshots support a model for biogenesis of the F transfer system and allow for detailed comparisons with other structurally characterized T4SSs.
Landscape Grain Effect in Yancheng Coastal Wetland and Its Response to Landscape Changes

The landscape grain effect reflects the spatial heterogeneity of a landscape and it is used as a research core of landscape ecology. The landscape grain effect can be used to not only explore spatiotemporal variation characteristics of a landscape pattern, but also to disclose variation laws of ecological structures and functions of landscapes. In this study, the sensitivity of landscape pattern indexes to grain sizes 50–1000 m was studied based on landscape data in Yancheng Coastal Wetland acquired in 1991, 2000, 2008, and 2017. Response of the grain effect to landscape changes was analyzed and an optimal grain size for analysis in the study area was determined. Results indicated that: (1) among 27 indexes (12 in a class level and 15 in a landscape level), eight indexes were highly sensitive to grains, ten indexes presented moderate sensitivity, eight indexes presented low sensitivity, and one was unresponsive. It was shown that the area-margin index and the shape index were more sensitive to the different grain sizes. The aggregation index had some differences in the grain size change, and the diversity index had a low response degree to the grain size. (2) Landscape indexes showed six different responses to different grains, including slow reduced response, fast reduced and then slow reduced response, monotonically increased response, fluctuating reduced response, up-down responses, and stable response, which indicated that the landscape index was closely related to the spatial grain. (3) From 1991 to 2017, variation curves of the landscape grain size of different landscape types could be divided into four types: fluctuation rising type, fluctuation type, monotonous decreasing type, and monotonous rising type. Different grain size curves had different interpretations of landscape changes, but in general, Yancheng Coastal Wetland’s landscape tended to be fragmented and complicated, internal connectivity was weakened, and dominant landscape area was reduced. Natural wetlands were more sensitive to grain size effects than artificial wetlands. (4) The landscape index at the 50 m grain size had a strong response to different grain size changes, and the loss of landscape information was the smallest. Therefore, it was determined that the optimal landscape grain size in the study area was 50 m.
Antenatal sonographic features of persistent extrahepatic vitelline vein aneurysm confused with umbilical vein varix

Abstract Background: The persistent vitelline vein is a portal venous system malformation arising during the embryonic period. These abnormal blood vessels frequently thrombose and can lead superior mesenteric vein obstruction or portal hypertension. Case report: We visualized a fetal intra-abdominal cystic mass with turbulent flow on prenatal ultrasound at 28 weeks’ gestation. Initially diagnosed as an umbilical vein varix, it was later determined to be an extrahepatic persistent vitelline vein with an internal thrombus by postnatal ultrasound. It was successfully surgically excised. Conclusion: When an abnormal abdominal vascular structure near the umbilicus is found during prenatal ultrasonography, the persistent vitelline vein should be included in the differential diagnosis to allow prompt evaluation and treatment after birth.
The Element of Surprise in Timed Games ⋆ In Proc. of CONCUR 2003: 14th International Conference on Concurrency Theory, Lectures Notes in Computer Science, Springer-Verlag, 2003.

We consider concurrent two-person games played in real time, in which the players decide both which action to play, and when to play it. Such timed games differ from untimed games in two essential ways. First, players can take each other by surprise, because actions are played with delays that cannot be anticipated by the opponent. Second, a player should not be able to win the game by preventing time from diverging. We present a model of timed games that preserves the ele- ment of surprise and accounts for time divergence in a way that treats both players symmetrically and applies to all ! -regular winning condi- tions. We prove that the ability to take each other by surprise adds extra power to the players. For the case that the games are specified in the style of timed automata, we provide symbolic algorithms for their so- lution with respect to all ! -regular winning conditions. We also show that for these timed games, memory strategies are more powerful than memoryless strategies already in the case of reachability objectives.
First-line treatment algorithm and guidelines in center-involving diabetic macular edema

Management of center-involving diabetic macular edema represents a real therapeutic challenge. Diabetic macular edema is the leading cause of visual acuity impairment in diabetic patients. Since the advent of intravitreal drugs, management of diabetic macular edema has significantly evolved. The historical grid laser photocoagulation is no longer recommended as first-line treatment of diabetic macular edema owing to the findings of the pivotal randomized controlled trials, and anti-vascular endothelial growth factor therapy has emerged as first-line therapy. Steroids also represent a valid treatment option in the management of naïve diabetic macular edema and their efficacy has also been confirmed in several studies. The optimal treatment for diabetic macular edema should consider both general and ophthalmological comorbidities. Patient compliance and motivation should also be carefully evaluated as some treatments require monthly follow-up. Based on recent literature evidence, the present review provides clinicians with a first-line treatment algorithm for center-involving diabetic macular edema tailored to the patient’s individual characteristics.
Ecological and Behavioural Flexibility of Mantled Howlers (Alouatta palliata) in Response to Anthropogenic Habitat Disturbance

While howlers are the most ecologically flexible of the atelines, they must still respond to issues arising from anthropogenic modifications, such as fragmentation or dietary changes. A group of Alouatta palliata living in a highly modified landscape (commensal group) at the Curú Wildlife Refuge in Costa Rica was compared to howlers with limited human influence (control group). The commensal group had a more frugivorous diet than the control group (H = 9.23, p = 0.002) due to crop-foraging of mango fruits. The commensal group maintained a larger home range than the control group, at 39 and 10 ha, respectively. The commensal group also had increased travel (H = 7.37, p = 0.007) and feeding (H = 7.34, p = 0.007) time, as well as reduced proximity to conspecifics (H = 44.77, p = 0.000). There were no significant differences in rates of either aggressive or affiliative social behaviours. The increased home range, shift in diet, increased travel and foraging time and reduced group cohesion demonstrated by these animals represent responses to the varied utility of available landscapes and the more widely dispersed resources in their range. These data contribute to our understanding of Alouatta, one of the most successful of Neotropical primates in modified landscapes.
Survey on Feature Selection in Document Clustering

Text mining is to research technologies to discover useful knowledge from enormous collections of documents, and to develop a system to provide knowledge and to support in decision making. Basically cluster means a group of similar data, document clustering means segregating the data into different groups of similar data. Clustering is a fundamental data analysis technique used for various applications such as biology, psychology, control and signal processing, information theory and mining technologies. Text mining is not a stand-alone task that human analysts typically engage in. The goal is to transform text composed of everyday language into a structured, database format. In this way, heterogeneous documents are summarized and presented in a uniform manner. Among others, the
Quorum sensing in Vibrio spp.: the complexity of multiple signalling molecules in marine and aquatic environments

Abstract Quorum sensing (QS) is a density-dependent mechanism enabling bacteria to coordinate their actions via the release of small diffusible molecules named autoinducers (AIs). Vibrio spp. are able to adapt to changing environmental conditions by using a wide range of physiological mechanisms and many species pose a threat for human health and diverse marine and estuarine ecosystems worldwide. Cell-to-cell communication controls many of their vital functions such as niche colonization, survival strategies, or virulence. In this review, I summarize (1) the different known QS pathways (2) the diversity of AIs as well as their biological functions, and (3) the QS-mediated interactions between Vibrio and other organisms. However, the current knowledge is limited to a few pathogenic or bioluminescent species and in order to provide a genus-wide view an inventory of QS genes among 87 Vibrio species has been made. The large diversity of signal molecules and their differential effects on a particular physiological function suggest that the complexity of multiple signalling systems within bacterial communities is far from being fully understood. I question here the real level of specificity of such communication in the environment and discuss the different perspectives in order to better apprehend QS in natural habitats.
Dribbling through the host defence: targeting the TLRs by pathogens

Abstract The immune system is well-equipped with sensors that detect invading pathogens and dictate subsequent immune responses for clearing the infections. One such class of sensor is the toll-like receptor (TLR), that can sense diverse molecules of pathogen origin such as proteins, lipids, carbohydrate, DNA, RNA, and trigger suitable immune responses to prevent infections. However, successful pathogens have evolved strategies to bypass the TLR-driven host immune responses to enable their survival inside the host. In this review, we have discussed about the recent advances in TLR biology and strategies adopted by various pathogens (bacteria, virus, and parasites) to subvert the TLR-signalling for evading host-immune attack. Further, we have discussed how TLRs are linked in augmenting infection burden and disease severity in host during co-infection. This information is likely to be helpful to design TLR-based immunotherapeutics to control various infections and pathophysiological disorders.
Solitary fibrous tumor of the cerebellopontine angle: A case report and literature review

Abstract Solitary fibrous tumors (SFT) are rare dura-based mesenchymal tumors of the central nervous system. SFT occurring in the cerebellopontine (CP) angle is very rare and only 21 cases have been reported in the literature until date. We present a 40-year-old male patient who presented with features of the right-sided facial and acoustic nerves paresis along with same sided cerebellar symptoms of 2 months duration. Magnetic resonance imaging revealed a T2 heterogeneously hyperintense extra-axial lesion, showing intense contrast enhancement in the right CP angle with solid and cystic areas. The lesion was not extending into the internal auditory canal. Digital subtraction angiography showed arterial feeders from vertebro-basilar system. The highly vascular lesion was excised near-totally by suboccipital retrosigmoid craniectomy. The lesion was diagnosed as SFT on histopathological examination and was positive for CD34 and bcl-2.
Role of chronic cannabis use: Cyclic vomiting syndrome vs cannabinoid hyperemesis syndrome

Cannabis is commonly used in cyclic vomiting syndrome (CVS) due to its antiemetic and anxiolytic properties. Paradoxically, chronic cannabis use in the context of cyclic vomiting has led to the recognition of a putative new disorder called cannabinoid hyperemesis syndrome (CHS). Since its first description in 2004, numerous case series and case reports have emerged describing this phenomenon. Although not pathognomonic, a patient behavior called “compulsive hot water bathing” has been associated with CHS. There is considerable controversy about how CHS is defined. Most of the data remain heterogenous with limited follow‐up, making it difficult to ascertain whether chronic cannabis use is causal, merely a clinical association with CVS, or unmasks or triggers symptoms in patients inherently predisposed to develop CVS. This article will discuss the role of cannabis in the regulation of nausea and vomiting, specifically focusing on both CVS and CHS, in order to address controversies in this context. To this objective, we have collated and analyzed published case series and case reports on CHS in order to determine the number of reported cases that meet current Rome IV criteria for CHS. We have also identified limitations in the existing diagnostic framework and propose revised criteria to diagnose CHS. Future research in this area should improve our understanding of the role of cannabis use in cyclic vomiting and help us better understand and manage this disorder.
Female adherence self-efficacy before and after couple HIV testing and counseling within Malawi’s Option B+ program

ABSTRACT Adherence self-efficacy, belief in one’s ability to adhere to daily medication, is strongly associated with antiretroviral therapy (ART) adherence and preventing mother-to-child HIV transmission. Couple-based interventions could enhance self-efficacy and adherence. We assessed the relationship between couple HIV testing and counseling (cHTC) and adherence self-efficacy using a 100-point culturally-adapted adherence self-efficacy scale (ASES). Secondarily, we explored the relationship between ASES and ART adherence. Ninety HIV-positive pregnant women at an antenatal clinic in Lilongwe, Malawi were enrolled in an observational cohort study. They were assessed with ASES immediately before and one month after receiving cHTC. Median ASES scores were 100 (IQR 95, 100) before and 100 (IQR 99, 100) after cHTC; there was a significant median difference (p = 0.02) for participants before and after cHTC. This change in ASES scores was associated with the odds of self-reported ART adherence in the full population (OR 1.1, p = 0.01), and there was a trend in the same direction for participants with imperfect baseline ASES scores (OR 1.1, p = 0.2). In our population, adherence self-efficacy and ART adherence were both quite high, and those who had room to improve in self-efficacy may have benefited from cHTC, which in turn could impact ART adherence and ultimately mother-to-child transmission.
Stem Cells for Extreme Prematurity

Abstract Regenerative medicine is a bourgeoning field promising to repair damaged organs and thus has created high hopes in neonatology to curb some of the complications due to extreme preterm birth. Extensive laboratory investigations over the past 15 years have tried to harness the regenerative potential of a variety of (stem) cell-based therapies. Most preclinical studies have focused on experimental neonatal lung and brain injury. These promising results lead to the initiation of phase I clinical trials for chronic lung disease of prematurity and severe intraventricular hemorrhage, two of the most devastating complications of extreme preterm birth. Despite this relative rapid clinical translation, major gaps persist in our understanding of the biology of these putative repair cells and our ability to predict the quality and thus the efficacy of the cell product. This review will provide a brief overview of the various cell-based therapies that have been investigated in experimental neonatal lung injury and the remaining challenges in utilizing these new, disruptive therapies to their full extend to realize the promise of regenerative medicine in neonatology.
Jacobi Iteration based Distributed Regression in Wireless Sensor Networks

Data modeling is a potential way of leveraging data spatio-temporal correlations for energy-saving data acquisition in wireless sensor networks (WSNs). This article presents energy-efficient Jacobi distributed algorithm for solving the algebraic equation towards to data regression modeling. In particular, the distributed iterative scheme is proposed to seek the solution of regression algebraic equation with the mixture representation of the regression model. In doing this, an elegant tree-based routing structure is employed to organize the nodes in coordination to accomplish the in-network implementation of the distributed iterative scheme. Under this routing scheme, the intersections among nodes are decoupled via asynchronous message passing protocol, which ensure each node can receive the exact decoupled information from local neighboring nodes for updating its local models. Rather than transmitting the raw sensed data to base station through the network, our Jacobi distributed algorithm provide an energy-saving data acquisition by only collecting the optimal weighted coefficients. The experimental results show that the method proposed here outperforms over the existing schemes in both computation costs and transmission requirements.
Dual role of FGF in proliferation and endoreplication of Drosophila tracheal adult progenitor cells

Abstract Adult progenitor cells activation is a key event in the formation of adult organs. In Drosophila, formation of abdominal adult trachea depends on the specific activation of tracheal adult progenitors (tracheoblasts) at the Tr4 and Tr5 spiracular branches. Proliferation of these tracheoblasts generates a pool of tracheal cells that migrate toward the posterior part of the trachea by the activation of the branchless/fibroblast growth factor (Bnl/FGF) signaling to form the abdominal adult trachea. Here, we show that, in addition to migration, Bnl/FGF signaling, mediated by the transcription factor Pointed, is also required for tracheoblast proliferation. This tracheoblast activation relies on the expression of the FGF ligand bnl in their nearby branches. Finally, we show that, in the absence of the transcription factor Cut (Ct), Bnl/FGF signaling induces endoreplication of tracheoblasts partially by promoting fizzy-related expression. Altogether, our results suggest a dual role of Bnl/FGF signaling in tracheoblasts, inducing both proliferation and endoreplication, depending on the presence or absence of the transcription factor Ct, respectively.
Asynchronous transfer of control in the Real-Time Specification for Java/sup TM/

The Real-Time Specification for Java provides a facility for asynchronous transfer of control based on exception handling and a generalization of the interrupt () method from the Thread class. This mechanism allows the programming of useful idioms such as timeouts and thread termination without the latency found in polling, and it avoids the problems inherent in the Thread class's stop () and destroy () methods.
Three-phase load flow methods for radial distribution networks

A distribution system has certain distinguishing features which make it different and somewhat difficult to analyze as compared to a transmission system. Unbalanced loads, untransposed lines, single-phase and two-phase laterals are some of them. The distribution system needs to be analyzed on the three-phase basis instead of the single-phase basis. Hence, the three-phase load flow for the distribution system is significantly different from the conventional load flow for the transmission system. In this paper, various load flow methods for distribution systems are reviewed. These methods are applied on a sample 8-bus system. The results are reported. The performance of these methods is compared for various parameters.
Understanding Collective Human Mobility Spatiotemporal Patterns on Weekdays from Taxi Origin-Destination Point Data

With the availability of large geospatial datasets, the study of collective human mobility spatiotemporal patterns provides a new way to explore urban spatial environments from the perspective of residents. In this paper, we constructed a classification model for mobility patterns that is suitable for taxi OD (Origin-Destination) point data, and it is comprised of three parts. First, a new aggregate unit, which uses a road intersection as the constraint condition, is designed for the analysis of the taxi OD point data. Second, the time series similarity measurement is improved by adding a normalization procedure and time windows to address the particular characteristics of the taxi time series data. Finally, the DBSCAN algorithm is used to classify the time series into different mobility patterns based on a proximity index that is calculated using the improved similarity measurement. In addition, we used the random forest algorithm to establish a correlation model between the mobility patterns and the regional functional characteristics. Based on the taxi OD point data from Nanjing, we delimited seven mobility patterns and illustrated that the regional functions have obvious driving effects on these mobility patterns. These findings are applicable to urban planning, traffic management and planning, and land use analyses in the future.