Miracle-dz/UniFAR-FTUs huggingface dataset:
Haemophilus spills its guts to make a biofilm

Most bacteria do not live as single cells but form communities on surfaces called biofilms (1). Similar to human communities, some are fairly homogeneous, whereas others contain a diversity of microbes. Biofilms are important for the growth and survival of all sorts of bacteria: bacteria that live in water or soil and also bacteria that live in or on animal hosts, including commensal bacteria, beneficial bacteria, and disease-causing bacteria (1). Biofilm communities are held together by a matrix containing a collection of molecules that are released by the bacterial cells within the biofilm (2). The composition of the biofilm matrix differs with different organisms but most often contains extracellular DNA (eDNA), polysaccharides, and proteins. The article in PNAS by Jurcisek et al. (3) demonstrates that nontypeable Haemophilus influenzae ( Hflu ) (4) uses components from two different secretion systems to release DNA and a biofilm-associated DNA-binding protein integration host factor (IHF) to allow efficient biofilm formation. This work shows that the secretion of DNA and DNABII proteins is an active process that uses components from two different apparatuses to enable robust biofilm formation. Bacteria are single-cell organisms that have a complex envelope structure that provides essential functions for the bacteria, including protecting the cell’s interior (cytoplasm) from injury, providing energy to the cell, maintaining the characteristic shape of each bacterial species, and mediating cell division (5). Most bacteria fall into two major classes based on their envelope architecture, gram-negative and gram-positive. There are six well-defined secretion systems in gram-negative bacteria (type I to VI); all can transport proteins into or outside of a bacterial cell, and a few can also transport DNA, often complexed with proteins (6). How the molecules that form biofilm matrixes are released from bacterial cells is not always understood, but it has been assumed, and in a few … [↵][1]1Email: h-seifert{at}northwestern.edu. [1]: #xref-corresp-1-1
A Precise Method for Cloth Configuration Parsing Applied to Single-Arm Flattening

In this paper, we investigate the contribution that visual perception affords to a robotic manipulation task in which a crumpled garment is flattened by eliminating visually detected wrinkles. In order to explore and validate visually guided clothing manipulation in a repeatable and controlled environment, we have developed a hand-eye interactive virtual robot manipulation system that incorporates a clothing simulator to close the effector-garment-visual sensing interaction loop. We present the technical details and compare the performance of two different methods for detecting, representing and interpreting wrinkles within clothing surfaces captured in high-resolution depth maps. The first method we present relies upon a clustering-based method for localizing and parametrizing wrinkles, while the second method adopts a more advanced geometry-based approach in which shape-topology analysis underpins the identification of the cloth configuration (i.e., maps wrinkles). Having interpreted the state of the cloth configuration by means of either of these methods, a heuristic-based flattening strategy is then executed to infer the appropriate forces, their directions and gripper contact locations that must be applied to the cloth in order to flatten the perceived wrinkles. A greedy approach, which attempts to flatten the largest detected wrinkle for each perception-iteration cycle, has been successfully adopted in this work. We present the results of our heuristic-based flattening methodology which relies upon clustering-based and geometry-based features respectively. Our experiments indicate that geometry-based features have the potential to provide a greater degree of clothing configuration understanding and, as a consequence, improve flattening performance. The results of experiments using a real robot (as opposed to simulated robot) also confirm our proposition that a more effective visual perception system can advance the performance of cloth manipulation.
Improving MAC layer association through social-based metrics in mobile networks

Mobile Social Network (MSN) is a social network where one or more elements share interests or commonalities by connecting with one another using mobile devices. However, contrary to traditional online social networks, efficient communication and information exchanged depends on mobile users' context. In order to increase the scalability of the information exchange, network nodes need to be associated and grouped through an efficient set of rules and criterions, to minimize the time and amount of data messages flowing in the network. This article shows how social-based metrics can increase the efficiency of layer 2 associations in mobile networks, where nodes are able to join the network through their context information and probable interactions, optimizing the information exchange at MAC layer. Through a case study of mobile communications with different mobility patterns and dissemination approaches, we show that the social-based metrics increase overall network efficiency: maximize the percentage of information delivery, decrease the time to disseminate data traffic and reduce network usage.
The effects of perceived daily social and academic failure experiences on school-age children's subsequent interactions with parents.

The hypothesis that perceived failure experiences at school would increase the likelihood of aversive parent-child interactions after school was supported in a study of 167 fourth, fifth, and sixth graders. Children completed measures of mood, school events, and parent-child interaction 3 times each day for 2 consecutive days. Reports of social and academic failure experiences at school (e.g., peer problems and difficulty with schoolwork) were associated with increases in child self-reports of demanding and aversive behavior toward parents that evening. There was no evidence of the reverse effect; aversive child behavior did not predict an increase in reports of negative events the next day. When children rated more academic failure events at school, they also described their parents as more disapproving and punishing after school. However, this effect was only partially mediated by increases in the child's aversive behavior. It is argued that the findings cannot be explained solely by a response bias caused by the child's general mood or frame of mind that day. First, school-to-home mood spillover effects were controlled in the analyses. Second, reports of problems at school were not associated with other aspects of parent-child interaction (e.g., the parent's positive behavioral and emotional involvement with the child). In addition to its substantive findings, the study illustrates use of an unbiased method for assessing child responses to daily stressors.
Microsatellites for Phytolacca acinosa (Phytolaccaceae), a traditional medicinal herb1

Premise of the study: Phytolacca acinosa (Phytolaccaceae) is a traditional Chinese herb with multiple medicinal uses and is an important pigment source. Due to excessive human harvesting, the population numbers and sizes have decreased dramatically. Methods and Results: Using an enriched genomic library, we developed and characterized 15 microsatellite primers for P. acinosa, 13 of which were polymorphic. The number of alleles varied from two to seven. The observed heterozygosity and expected heterozygosity per locus ranged from 0.267 to 1.000 and 0.331 to 0.743, respectively. All of the primers that were developed were also successfully applied in P. americana. Conclusions: These markers should be useful in probing the genetic diversity, genetic structure, and mating systems of P. acinosa, which could provide information about protecting and sustainably harvesting this species.
The N-terminal part of the E.coli DNA binding protein FIS is essential for stimulating site-specific DNA inversion but is not required for specific DNA binding.

FIS protein is involved in several different cellular processes stimulating site-specific recombination in phages Mu and lambda as well as transcription of stable RNA operons in E.coli. We have performed a mutational analysis of fis and provide genetic and biochemical evidence that a truncated version of FIS lacking the N-terminal region is sufficient for specific DNA binding and for stimulating lambda excision. These mutants also retain their ability to autoregulate fis gene expression. Such mutant proteins, however, cannot stimulate the enhancer dependent DNA inversion reaction.
Abrupt Alnus population decline at the end of the first millennium CE in Europe – The event ecology, possible causes and implications

The study, based on the examination of 70 published and unpublished pollen profiles from Poland and supplementary data from the surrounding regions, shows that an abrupt, episodic Alnus population decline at the end of the first millennium CE was a much more widespread event than has been previously reported, spanning large areas of the temperate and boreal zones in Europe. The data from Poland suggest that the decline was roughly synchronous and most likely occurred between the 9th and 10th centuries, with strong indications for the 10th century. The pollen data indicate that human impacts were not a major factor in the event. Instead, we hypothesize that one or a series of abrupt climatic shifts that caused floods and droughts at the end of the first millennium CE could have initiated this ecological disturbance, leading to a higher vulnerability of the alder trees to a pathogen outbreak. Following current observations of the decline of alder stands in Europe due to a Phytophthora outbreak, we suggest that a similar process may have occurred in the past. This study provides insight into long-term alder (mainly Alnus glutinosa) dynamics in a condition of climate change and illustrates its great resilience, enabling the natural, successful regeneration of alder stands after critical diebacks if environmental conditions improve. Our finding that the Alnus pollen decline reflects a roughly synchronous event indicates that the decline could be used as an over-regional chronostratigraphic marker for 800–1000 CE in pollen diagrams from a large part of the European Lowland.
pH modulation of currents that contribute to the medium and slow afterhyperpolarizations in rat CA1 pyramidal neurones

We examined the effects of changes in pHo and pHi on currents contributing to the medium and slow afterhyperpolarizations (mIAHP and sIAHP, respectively) in rat CA1 neurones. Reducing pHo from 7.4 to 6.7 inhibited mIAHP and sIAHP whereas increasing pHo to 7.7 augmented mIAHP and, to a greater extent, sIAHP. The ability of changes in pHo to modulate mIAHP reflected changes in the Ca2+‐activated K+ current, IAHP, and a Co2+‐ and XE991‐resistant component of mIAHP, but not the muscarine‐sensitive current, IM. In the presence of 1 μm TTX and 5 mm TEA, low pHo‐evoked reductions in sIAHP were associated with reductions in Ca2+‐dependent depolarizing potentials; because neither effect was attenuated when internal H+ buffering power was raised by including 100 mm tricine in the patch pipette, the actions of reductions in pHo to inhibit sIAHP and, possibly, IAHP in large part appear to reflect a low pHo‐dependent decrease in Ca2+ influx. In contrast, the effects of high pHo to augment mIAHP and sIAHP were associated with relatively small increases in Ca2+ potentials but were significantly attenuated by 100 mm internal tricine, indicating that a rise in pHi consequent upon the rise in pHo was largely responsible. The possibility that changes in pHi could act to modulate mIAHP and sIAHP, independently of changes in Ca2+ influx, was also suggested by experiments in which pHi was lowered at a constant pHo by the external application of propionate or by the withdrawal of HCO−3 from the perfusing medium. Lowering pHi at a constant pHo had little effect on Ca2+ potentials but inhibited mIAHP and, to a greater extent, sIAHP, effects that were attenuated by 100 mm internal tricine. Together, the results indicate that changes in pHo and pHi modulate mIAHP and sIAHP in rat CA1 neurones and suggest that, depending on the direction of the pHo change, the sensitivities of the underlying currents to changes in Ca2+ influx and/or pHi may contribute to the effects of changes in pHo to modulate mIAHP and sIAHP.
The effect of moderate intensity exercise on the activity of catalase enzyme and malondialdehyde in hippocampus area of diabetic male Wistar rats

: Background: Diabetes mellitus exacerbates oxidative stress and reduces the antioxidant defense system activity. As the brain has a high sensitivity to oxidative stress due to physiological and biochemical reasons and scientific evidence suggests the effect of regular exercise on reducing brain sensitivity to brain damage under pathophysiological conditions. Therefore, this study aimed at investigating the effect of moderate intensity exercise training on the activity of catalase enzyme and malondialdehyde in hippocampus area of diabetic male Wistar rats. Materials and Methods: Twenty-four male rats (245±9.4 g) aged 10 weeks were divided into four groups (diabetic training, diabetic control, healthy training and healthy control). The rats of the diabetic group were diabetic by intraperitoneal injection of streptozotocin (STZ). The exercise program included 6 weeks of moderate intensity exercise. At the end of six weeks, the hippocampal tissue samples were extracted 24 hours after the last training session and the activity of catalase enzyme and malondialdehyde was evaluated. Results: After the endurance training, the catalase levels in both diabetic training group (161.24±7.74) compared to the diabetic control group (148.55±8.05) and healthy training group (408.85±2.3) compared to the healthy control group (283.44±9.33) were significantly increased ( P <0.05). Also, the level of malondialdehyde in the diabetic training group (9.65±1.75) was significantly decreased compared to the control diabetic group (13.23±1.01) ( P > 0.05). Conclusion: It can be concluded that endurance training may be effective to increase the antioxidant role of catalase enzyme and reduce the amount of malondialdehyde in the hippocampus tissue of diabetic rats.
Developmental apoptosis in the spinal cord white matter in neonatal rats

We investigated developmental apoptosis in the white matter of the cervical spinal cord at postnatal days 2, 5, and 8. Apoptotic cells were labeled using TUNEL and caspase‐3 immunostaining. Apoptotic cells were diffusely distributed throughout the white matter of the spinal cord. The total amount of apoptotic cells in the cervical spinal cord white matter was related to postnatal age, with the lowest at P2 (mean 7.9, SD 5.6) and the highest at P8 (mean 109, SD 21.4). Using double immunostaining for ED‐1 and O4, apoptotic cells were identified as microglia and oligodendrocytes. GLIA 37:89–91, 2002. © 2002 Wiley‐Liss, Inc.
Differential roles of XRCC2 in homologous recombinational repair of stalled replication forks

Homologous recombination is an important mechanism in DNA replication to ensure faithful DNA synthesis and genomic stability. In this study, we investigated the role of XRCC2, a member of the RAD51 paralog family, in cellular recovery from replication arrest via homologous recombination. The protein expression of XRCC2, as well as its binding partner RAD51D, is dramatically increased in S‐ and G2‐phases, suggesting that these proteins function during and after DNA synthesis. XRCC2 mutant irs1 cells exhibit hypersensitivity to hydroxyurea (HU) and are defective in the induction of RAD51 foci after HU treatment. In addition, the HU‐induced chromatin association of RAD51 is deficient in irs1 mutant. Interestingly, irs1 cells are only slightly sensitive to thymidine and able to form intact RAD51 foci in S‐phase cells arrested with thymidine. Irs1 cells showed increased level of chromatin‐bound RAD51 as well as the wild type cells after thymidine treatment. Both HU and thymidine induce γ‐H2AX foci in arrested S‐phase nuclei. These results suggest that XRCC2 is involved in repair of HU‐induced damage, but not thymidine‐induced damage, at the stalled replication forks. Our data suggest that there are at least two sub‐pathways in homologous recombination, XRCC2‐dependent and ‐independent, for repair of stalled replication forks and assembly of RAD51 foci following replication arrest in S‐phase. © 2005 Wiley‐Liss, Inc.
Brain–computer interface control along instructed paths

Objective. Brain–computer interfaces (BCIs) are being developed to assist paralyzed people and amputees by translating neural activity into movements of a computer cursor or prosthetic limb. Here we introduce a novel BCI task paradigm, intended to help accelerate improvements to BCI systems. Through this task, we can push the performance limits of BCI systems, we can quantify more accurately how well a BCI system captures the user’s intent, and we can increase the richness of the BCI movement repertoire. Approach. We have implemented an instructed path task, wherein the user must drive a cursor along a visible path. The instructed path task provides a versatile framework to increase the difficulty of the task and thereby push the limits of performance. Relative to traditional point-to-point tasks, the instructed path task allows more thorough analysis of decoding performance and greater richness of movement kinematics. Main results. We demonstrate that monkeys are able to perform the instructed path task in a closed-loop BCI setting. We further investigate how the performance under BCI control compares to native arm control, whether users can decrease their movement variability in the face of a more demanding task, and how the kinematic richness is enhanced in this task. Significance. The use of the instructed path task has the potential to accelerate the development of BCI systems and their clinical translation.
Influence of landscape context on the abundance and diversity of bees in Mediterranean olive groves

Abstract The diversity and abundance of wild bees ensures the delivery of pollination services and the maintenance of ecosystem diversity. As previous studies carried out in Central Europe and the US have shown, bee diversity and abundance is influenced by the structure and the composition of the surrounding landscape. Comparable studies have so far not been carried out in the Mediterranean region. The present study examines the influence of Mediterranean landscape context on the diversity and abundance of wild bees. To do this, we sampled bees in 13 sites in olive groves on Lesvos Island, Greece. Bees were assigned to five categories consisting of three body size groups (small, medium and large bees), the single most abundant bee species (Lasioglossum marginatum) and all species combined. The influence of the landscape context on bee abundance and species richness was assessed at five radii (250, 500, 750, 1000 and 1250 m) from the centre of each site. We found that the abundance within bee groups was influenced differently by different landscape parameters and land covers, whereas species richness was unaffected. Generally, smaller bees’ abundance was impacted by landscape parameters at smaller scales and larger bees at larger scales. The land cover that influenced bee abundance positively was olive grove, while phrygana, conifer forest, broad-leaved forest, cultivated land, rock, urban areas and sea had mostly negative or no impact. We stress the need for a holistic approach, including all land covers, when assessing the effects of landscape context on bee diversity and abundance in the Mediterranean.
A Quick Scatter Search

The evolutionary approach called Scatter Search (SS) is successful in its theory and applications. However, SS has some shortcomings such as initial population scattered less evenly over the feasible solution space, the poor ability of finding global optima and the large number of objective function evaluations, so that we design an evolutionary algorithm called the Quick Scatter Search (QSS). QSS combines an orthogonal design method with SS to improve the shortcomings and satisfy the needs of practical projects. The experimental results prove that the proposed algorithm is superior to SS. Not only is QSS the number of its objective function evaluations less and the velocity of its convergence faster than SS, but also it is quicker to find global optimal solutions and even extremely close-to-optimal global solutions. Especially, the performance of QSS is better than that of SS in high dimension space.
Hybrid rotors in F1Fo ATP synthases: subunit composition, distribution, and physiological significance

Abstract The c ring of the Na+ F1Fo ATP synthase from the anaerobic acetogenic bacterium Acetobacterium woodii is encoded by three different genes: atpE1, atpE2 and atpE3. Subunit c1 is similar to typical V-type c subunits and has four transmembrane helices with one ion binding site. Subunit c2 and c3 are identical at the amino acid level and are typical F-type c subunits with one ion binding site in two transmembrane helices. All three constitute a hybrid FoVo c ring, the first found in nature. To analyze whether other species may have similar hybrid rotors, we searched every genome sequence publicly available as of 23 February 2015 for F1Fo ATPase operons that have more than one gene encoding the c subunit. This revealed no other species that has three different c subunit encoding genes but twelve species that encode one Fo- and one Vo-type c subunit in one operon. Their c subunits have the conserved binding motif for Na+. The organisms are all anaerobic. The advantage of hybrid c rings for the organisms in their environments is discussed.
Vehicle to Internet communications using the ETSI ITS GeoNetworking protocol

Vehicular ad hoc networks allow the exchange of information between vehicles to improve road safety. In addition, vehicles can be connected to the Internet through gateways placed alongside the roads, which allow drivers to use common Internet services and new applications specifically oriented to them. The European Telecommunications Standards Institute Technical Committee Intelligent Transport System has standardised the architecture and the communication protocols for an Intelligent Transport System, considering both safety applications and communications with the Internet. The GeoNetworking (GN) protocol has been designed to forward packets inside the vehicular ad hoc network taking safety requirements as the main concern. This paper analyses the GN protocol focusing on the provision of Internet connectivity to vehicles. The main contributions of this work are the identification of sources of performance losses when using the GN protocol in communications with the Internet and the proposal of different mechanisms to improve its performance in this type of communications. The evaluation of the GN protocol and the proposed improvements is conducted by means of extensive simulations. Copyright © 2014 John Wiley & Sons, Ltd.