Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the Fine Details of C1 Assembly and Activation Mechanisms: “Mission Impossible”?

The classical complement pathway is initiated by the large (~800 kDa) and flexible multimeric C1 complex. Its catalytic function is triggered by the proteases hetero-tetramer C1r2s2, which is associated to the C1q sensing unit, a complex assembly of 18 chains built as a hexamer of heterotrimers. Initial pioneering studies gained insights into the main architectural principles of the C1 complex. A dissection strategy then provided the high-resolution structures of its main functional and/or structural building blocks, as well as structural details on some key protein–protein interactions. These past and current discoveries will be briefly summed up in order to address the question of what is still ill-defined. On a functional point of view, the main molecular determinants of C1 activation and its tight control will be delineated. The current perspective remains to decipher how C1 really works and is controlled in vivo, both in normal and pathological settings.
Hamilton cycles in quasirandom hypergraphs

We show that, for a natural notion of quasirandomness in k‐uniform hypergraphs, any quasirandom k‐uniform hypergraph on n vertices with constant edge density and minimum vertex degree Ω(nk‐1) contains a loose Hamilton cycle. We also give a construction to show that a k‐uniform hypergraph satisfying these conditions need not contain a Hamilton ℓ‐cycle if k– ℓ divides k. The remaining values of ℓ form an interesting open question. © 2016 Wiley Periodicals, Inc. Random Struct. Alg. , 49, 363–378, 2016
The treatment of patent ductus arteriosus in preterm infants. A review and overview of randomized trials.

Patent ductus arteriosus (PDA) is a common problem in very preterm infants. It results in a significant left-to-right shunt and an increase in left ventricular output. Pulmonary compliance can be reduced. Systemic effects result from the diastolic steal and retrograde diastolic blood flow. Randomized controlled trials of PDA closure fall into three groups: (i) prophylactic treatment in the first 24 h, (ii) pre-symptomatic treatment on ultrasound evidence of a PDA or the first clinical signs and (iii) treatment when it becomes haemodynamically significant. Prophylactic treatment with indomethacin reduces the incidence of intraventricular haemorrhage. All the trials have a decreased need to treat a subsequent PDA in the treatment group. There are no other improvements in outcome, without any change in mortality, bronchopulmonary dysplasia, necrotizing enterocolitis or retinopathy of prematurity. Clinical decisions on the treatment of the ductus should be individualized and based on the gestation of the baby, the respiratory condition and the size of the ductal shunt.
Solving parametric algebraic systems

For a parametric polynomial system: p1 = 0, · · · , pr = 0, d1 6= 0, · · · , ds 6= 0 where pi and di are in K[u1, · · · , um, x1, · · · , xn] and the u are parameters, we present a method for identifying all parametric values for which the system has solutions for the xi and at the same time giving the solutions (for the xi) of the system in an explicit way, i.e., the solutions are given by polynomial sets in triangular form. The algorithm has been implemented and several examples reported in this paper show the algorithm is of practical value.
Don’t Get Me Wrong: ERP Evidence from Cueing Communicative Intentions

How to make sure that one’s utterances are understood as intended when not facing each other? In order to convey communicative intentions, in digital communication emoticons and pragmatic cues are frequently used. Such cueing becomes even more crucial for implied interpretations (e.g., irony) that cannot be understood literally, but require extra information. Sentences, such as ‘That’s fantastic,’ may achieve either a literal or ironic meaning depending on the contextual constraints. In two experiments using event-related brain potentials (ERPs), we examined the effects of cueing communicative intentions (i.e., by means of quotation marks) on ironic and literal language comprehension. An impact of cueing on language processing was seen as early as 200 ms post-stimulus onset by the emergence of a P300 preceding a sustained positivity for cued irony relative to literal language, while for uncued irony a P200-P600 pattern was obtained. In presence of additional information for ironic intentions, pragmatic reanalysis allowing inferences on the message level may have occured immediately. Moreover, by examining the way of cueing (i.e., ambiguous vs. unambiguous cueing) this type of information for communicative intentions appeared to be only effective when the cues were unambiguous by matching pragmatic conventions. The findings suggest that cueing communicative intentions may immediately affect language comprehension, albeit depending on pragmatic conventions of the cues’ usage.
Connectionist Perspectives on Category-Specific Deficits

Theories of semantic memory tend between two poles. At one extreme is a view often associated with the connectionist enterprise: that the semantic system is a unitary, homogeneous mass, without functional or neuroanatomic specialisation, that capitalises on statistical regularities in the environment in learning about and processing semantic information. On this account, double dissociations of semantic memory are explained in terms of the processing mechanisms characteristic of neural networks, the statistical structure of the environment, and various psycholinguistic factors such as familiarity, frequency, and visual complexity. At the other extreme is a view positing that semantic memory is parcelled functionally and neuroanatomically into a set of discrete processing modules, each tied to a particular modality and/or semantic domain. Under this hypothesis, double dissociations of semantic memory arise from damage to one or another of these modules, or the connections between them.
An Optimization Algorithm for the Ordered Open-End Bin-Packing Problem

The ordered open-end bin-packing problem is a variant of the bin-packing problem in which the items to be packed are sorted in a given order and the capacity of each bin can be exceeded by the last item packed into the bin. We present a branch-and-price algorithm for its exact optimization. The pricing subproblem is a special variant of the binary knapsack problem, in which the items are ordered and the last one does not consume capacity. We present a specialized optimization algorithm for this subproblem. The speed of the column generation algorithm is improved by subgradient optimization steps, allowing for multiple pricing and variable fixing. Computational results are presented on instances of different sizes and items with different correlations between their size and their position in the given order.
Laparoscopic vs conventional Nissen fundoplication. A prospective randomized study.

BACKGROUND Laparoscopic Nissen fundoplication has gained wide acceptance among surgeons, but the results of the laparoscopic procedure have not been compared to the results of an open fundoplication in a randomized study. METHODS Some 110 consecutive patients with prolonged symptoms of grade II-IV esophagitis were randomized, 55 to laparoscopic (LAP) and 55 to an open (OPEN) Nissen fundoplication. Postoperative recovery, complications, and outcome at 3- and 12-month follow-up were compared in the two groups. RESULTS Five LAP operations were converted to open laparotomy due to esophageal perforation (two), technical difficulties (two), and bleeding (one). In the OPEN group (two) patients underwent splenectomy. There was no mortality. The mean hospital stay was 3.2 days in the LAP group and 6.4 in the OPEN group. Dysphagia and gas bloating were the most common complaints 3 months after the operation in both groups. These symptoms had disappeared at the 12-month follow-up examination. All patients in the LAP group and 86% in the OPEN group were satisfied with the result. CONCLUSIONS Laparoscopic Nissen fundoplication is a safe and feasible procedure. Complications are few and functional results are good if not better than those of conventional open surgery.
Biofilm formation by the probiotic Lactobacillus rhamnosus GG : impact of 1 environmental and genetic factors 2 3 Running title : Biofilm formation by L . rhamnosus GG 4 5

Biofilm formation by the probiotic Lactobacillus rhamnosus GG: impact of 1 environmental and genetic factors 2 3 Running title: Biofilm formation by L. rhamnosus GG 4 5 Sarah Lebeer, Tine L.A. Verhoeven, Mónica Perea Vélez, Jos Vanderleyden, Sigrid C.J. 6 De Keersmaecker* 7 8 Centre of Microbial and Plant Genetics, K.U. Leuven, Kasteelpark Arenberg 20, 3001 9 Leuven, Belgium 10 11
Increase of TREM2 during Aging of an Alzheimer’s Disease Mouse Model Is Paralleled by Microglial Activation and Amyloidosis

Heterozygous missense mutations in the triggering receptor expressed on myeloid cells 2 (TREM2) have been reported to significantly increase the risk of developing Alzheimer’s disease (AD). Since TREM2 is specifically expressed by microglia in the brain, we hypothesized that soluble TREM2 (sTREM2) levels may increase together with in vivo biomarkers of microglial activity and amyloidosis in an AD mouse model as assessed by small animal positron-emission-tomography (μPET). In this cross-sectional study, we examined a strong amyloid mouse model (PS2APP) of four age groups by μPET with [18F]-GE180 (glial activation) and [18F]-florbetaben (amyloidosis), followed by measurement of sTREM2 levels and amyloid levels in the brain. Pathology affected brain regions were compared between tracers (dice similarity coefficients) and pseudo-longitudinally. μPET results of both tracers were correlated with terminal TREM2 levels. The brain sTREM2 levels strongly increased with age of PS2APP mice (5 vs. 16 months: +211%, p < 0.001), and correlated highly with μPET signals of microglial activity (R = 0.89, p < 0.001) and amyloidosis (R = 0.92, p < 0.001). Dual μPET enabled regional mapping of glial activation and amyloidosis in the mouse brain, which progressed concertedly leading to a high overlap in aged PS2APP mice (dice similarity 67%). Together, these results substantiate the use of in vivo μPET measurements in conjunction with post mortem sTREM2 in future anti-inflammatory treatment trials. Taking human data into account sTREM2 may increase during active amyloid deposition.
Gait Transitions in Human Infants: Coping with Extremes of Treadmill Speed

Spinal pattern generators in quadrupedal animals can coordinate different forms of locomotion, like trotting or galloping, by altering coordination between the limbs (interlimb coordination). In the human system, infants have been used to study the subcortical control of gait, since the cerebral cortex and corticospinal tract are immature early in life. Like other animals, human infants can modify interlimb coordination to jump or step. Do human infants possess functional neuronal circuitry necessary to modify coordination within a limb (intralimb coordination) in order to generate distinct forms of alternating bipedal gait, such as walking and running? We monitored twenty-eight infants (7–12 months) stepping on a treadmill at speeds ranging between 0.06–2.36 m/s, and seventeen adults (22–47 years) walking or running at speeds spanning the walk-to-run transition. Six of the adults were tested with body weight support to mimic the conditions of infant stepping. We found that infants could accommodate a wide range of speeds by altering stride length and frequency, similar to adults. Moreover, as the treadmill speed increased, we observed periods of flight during which neither foot was in ground contact in infants and in adults. However, while adults modified other aspects of intralimb coordination and the mechanics of progression to transition to a running gait, infants did not make comparable changes. The lack of evidence for distinct walking and running patterns in infants suggests that the expression of different functional, alternating gait patterns in humans may require neuromuscular maturation and a period of learning post-independent walking.
Differential changes in gene expression in human neutrophils following TNF‐α stimulation: Up‐regulation of anti‐apoptotic proteins and down‐regulation of proteins involved in death receptor signaling

Responses of human neutrophils to TNF‐α are complex and multifactorial. Exposure of human neutrophils to TNF‐α in vitro primes the respiratory burst, delays apoptosis and induces the expression of several genes including chemokines, and TNF‐α itself. This study aimed to determine the impact of TNF‐α exposure on the expression of neutrophil genes and proteins that regulate apoptosis. Quantitative PCR and RNA‐Seq, identified changes in expression of several apoptosis regulating genes in response to TNF‐α exposure. Up‐regulated genes included TNF‐α itself, and several anti‐apoptotic genes, including BCL2A1, CFLAR (cFLIP) and TNFAIP3, whose mRNA levels increased above control values by between 4‐20 fold (n = 3, P < 0.05). In contrast, the expression of pro‐apoptotic genes, including CASP8, FADD and TNFRSF1A and TNFRSF1B, were significantly down‐regulated following TNF‐α treatment. These changes in mRNA levels were paralleled by decreases in protein levels of caspases 8 and 10, TRADD, FADD, TNFRSF1A and TNFRSF1B, and increased cFLIP protein levels, as detected by western blotting. These data indicate that when neutrophils are triggered by TNF‐α exposure, they undergo molecular changes in transcriptional expression to up‐regulate expression of specific anti‐apoptotic proteins and concomitantly decrease expression of specific proteins involved in death receptor signaling which will alter their function in TNF‐α rich environments.
Differential Response of Human Nasal and Bronchial Epithelial Cells Upon Exposure to Size-Fractionated Dairy Dust

Exposure to organic dusts is associated with increased respiratory morbidity and mortality in agricultural workers. Organic dusts in dairy farm environments are complex, polydisperse mixtures of toxic and immunogenic compounds. Previous toxicological studies focused primarily on exposures to the respirable size fraction; however, organic dusts in dairy farm environments are known to contain larger particles. Given the size distribution of dusts from dairy farm environments, the nasal and bronchial epithelia represent targets of agricultural dust exposures. In this study, well-differentiated normal human bronchial epithelial cells and human nasal epithelial cells were exposed to two different size fractions (PM10 and PM>10) of dairy parlor dust using a novel aerosol-to-cell exposure system. Levels of proinflammatory transcripts (interleukin [IL]-8, IL-6, and tumor necrosis factor [TNF]-α) were measured 2 h after exposure. Lactate dehydrogenase (LDH) release was also measured as an indicator of cytotoxicity. Cell exposure to dust was measured in each size fraction as a function of mass, endotoxin, and muramic acid levels. To our knowledge, this is the first study to evaluate the effects of distinct size fractions of agricultural dust on human airway epithelial cells. Our results suggest that both PM10 and PM>10 size fractions elicit a proinflammatory response in airway epithelial cells and that the entire inhalable size fraction needs to be considered when assessing potential risks from exposure to agricultural dusts. Further, data suggest that human bronchial cells respond differently to these dusts than human nasal cells, and therefore that the two cell types need to be considered separately in airway cell models of agricultural dust toxicity.
A Flexible Software Radio Transceiver for UHF RFID Experimentation : UW TR : UW-CSE-09-1002

We present the design and evaluation of a flexible UHF RFID reader suited for experimentation. Our reader is built using the USRP software radio platform in conjunction with software we developed in the GNU Radio framework. We believe this is the first inexpensive tool that readily enables changes to the physical and MAC layer of RFID systems. Our reader further has sufficient performance to interoperate with commercial EPC Gen-2 RFID tags and achieves roughly 75% of the range of a commercial reader with comparable power. To support communication with commodity RFID tags, we aggressively reduced system latency from the 10s of milliseconds typical of USRP applications to consistently under 500 μs.
The Lymphocytic Choriomeningitis Virus Matrix Protein PPXY Late Domain Drives the Production of Defective Interfering Particles

Arenaviruses cause severe diseases in humans but establish asymptomatic, lifelong infections in rodent reservoirs. Persistently-infected rodents harbor high levels of defective interfering (DI) particles, which are thought to be important for establishing persistence and mitigating virus-induced cytopathic effect. Little is known about what drives the production of DI particles. We show that neither the PPXY late domain encoded within the lymphocytic choriomeningitis virus (LCMV) matrix protein nor a functional endosomal sorting complex transport (ESCRT) pathway is absolutely required for the generation of standard infectious virus particles. In contrast, DI particle release critically requires the PPXY late domain and is ESCRT-dependent. Additionally, the terminal tyrosine in the PPXY motif is reversibly phosphorylated and our findings indicate that this posttranslational modification may regulate DI particle formation. Thus we have uncovered a new role for the PPXY late domain and a possible mechanism for its regulation.
Survive and Extravasate Fate of Melanoma Cells Entering the Microcirculation : Over 80 % Updated

Metastasis is an inefficient process; only a few cancer cells are able to form tumors after being released into the circulation. We studied the fate of cancer cells after injection into the circulation, quantifying their sur vival and ability to extravasate by 1 day later, li 161 10 cells, parental or transfectants overexpressing tissue inhibitor of metalloproteinases 1, were injected i.v. into chorioallantoic membrane of chick embryos and analyzed by intravital videomicroscopy. Cell survival was quantified in two ways: (a) 15-um microspheres were injected with cancer cells, and proportions of viable cells to microspheres were compared before and after injection; and (b) individual cancer cells were monitored continuously for 0.5-8-h intervals covering the first 24 h. Both methods showed virtually no destruction of cells. Greater than 80% of injected cells survived and extravasated by 24 h, indicating that growth after extravasation is a key stage of metastatic control.
A Scalable Mark-Sweep Garbage Collector on Large-Scale Shared-Memory Machines

This work describes implementation of a mark-sweep garbage collector (GC) for shared-memory machines and reports its performance. It is a simple 'parallel' collector in which all processors cooperatively traverse objects in the global shared heap. The collector stops the application program during a collection. To achieve scalability, collector performs dynamic load balancing, which exchanges objects to be scanned between processors. However, we observed that the implementation detail affects the performance heavily. For example, large objects, which become a source of significant load imbalance are split into small pieces. With all careful implementation, we achieved 28-fold speed-up on 64 processors.
The impact of trade liberalisation on the informal sector in Brazil

We assess whether or not the trade liberalisation process in Brazil had any effect on both the reduction in the wage differential between registered and non-registered (roughly formal and informal) workers and the fall in the proportion of registered workers. We discuss the channels through which trade liberalisation could affect these two variables and put forward three empirical approaches to test the existence of any correlation between them. Our results suggest that the fall in the wage gap between registered and non-registered workers in the manufacturing sector was affected by trade-related variables, particularly, by the import penetration ratio. However, we do not find robust evidence that trade liberalisation had a substantial effect on the fall in the proportion of registered workers.
Modest doses of beta-glucan do not reduce concentrations of potentially atherogenic lipoproteins.

BACKGROUND In 1997, the US Food and Drug Administration passed a unique ruling that allowed oat bran to be registered as the first cholesterol-reducing food at a dosage of 3 g beta-glucan/d. OBJECTIVE The effects of a low dose of oat bran in the background diet only were investigated in volunteers with mild-to-moderate hyperlipidemia. DESIGN The study was a double-blind, placebo-controlled, randomized, parallel study. Sixty-two healthy men (n = 31) and women (n = 31) were randomly allocated to consume either 20 g oat bran concentrate (OBC; containing 3 g beta-glucan) or 20 g wheat bran (control) daily for 8 wk. Fasting blood samples were collected at weeks -1, 0, 4, 8, and 12. A subgroup (n = 17) was studied postprandially after consumption of 2 meals (containing no OBC or wheat bran) at baseline and after supplementation. Fasting plasma samples were analyzed for total cholesterol, HDL cholesterol, triacylglycerol, glucose, and insulin. LDL cholesterol was measured by using the Friedewald formula. The postprandial samples were anlayzed for triacylglycerol, glucose, and insulin. RESULTS No significant difference was observed in fasting plasma cholesterol, LDL cholesterol, glucose, or insulin between the OBC and wheat-bran groups. HDL-cholesterol concentrations fell significantly from weeks 0 to 8 in the OBC group (P = 0.05). There was a significant increase in fasting glucose concentrations after both OBC (P = 0.03) and wheat-bran (P = 0.02) consumption. No significant difference was found between the OBC and wheat-bran groups in any of the postprandial variables measured. CONCLUSIONS A low dosage of beta-glucan (3 g/d) did not significantly reduce total cholesterol or LDL cholesterol in volunteers with plasma cholesterol concentrations representative of a middle-aged UK population.
A call for full annual cycle research in animal ecology

For vertebrates, annual cycles are organized into a series of breeding and non-breeding periods that vary in duration and location but are inextricably linked biologically. Here, we show that our understanding of the fundamental ecology of four vertebrate classes has been limited by a severe breeding season research bias and that studies of individual and population-level responses to natural and anthropogenic change would benefit from a full annual cycle perspective. Recent emergence of new analytical and technological tools for studying individual and population-level animal movement could help reverse this bias. To improve understanding of species biology and reverse the population declines of many vertebrate species, a concerted effort to move beyond single season research is vital.