Miracle-dz/UniFAR-FTUs huggingface dataset:
Census Signal Temporal Logic Inference for Multiagent Group Behavior Analysis

In this paper, we define a novel census signal temporal logic (CensusSTL) that focuses on the number of agents in different subsets of a group that complete a certain task specified by the STL. CensusSTL consists of an “<italic>inner logic</italic>” STL formula and an “<italic>outer logic</italic>” STL formula. We present a new inference algorithm to infer CensusSTL formulas from the trajectory data of a group of agents. We first identify the “<italic>inner logic</italic>” STL formula and then infer the subgroups based on whether the agents’ behaviors satisfy the “<italic>inner logic</italic>” formula at each time point. We use two different approaches to infer the subgroups based on similarity and complementarity, respectively. The “<italic>outer logic</italic>” CensusSTL formula is inferred from the census trajectories of different subgroups. We apply the algorithm in analyzing data from a soccer match by inferring the CensusSTL formula for different subgroups of a soccer team. </p><p><italic>Note to Practitioners</italic>—The method described in this paper can be used to discover subgroups of agents and their behavior patterns based on spatial–temporal data of all agents in the group. The subgroups are formed by agents that behave similarly or complementarily for a certain task. The behavior patterns of the subgroups are expressed in the form of signal temporal logic statements. These are logical statements about the number of agents in the subgroups that are in certain states during a certain time interval. For example, if there are more than two blue agents in the region, then within 2 h, there will be more than three red agents in the same region. The behavior patterns inferred using this method can be used in: 1) analysis of group behavior while performing a task, e.g., in sports tactical analysis and 2) prediction of future group behavior under similar situations.
Flow Cytometry in the Detection of Neonatal Sepsis

Neonatal sepsis remains a burden problem by showing minimal initial symptoms of subtle character, nonspecific manifestation, and diagnostic pitfalls. The clinical course can be fulminant and fatal if treatment is not commenced promptly. It is therefore crucial to establish early diagnosis and initiate adequate therapy. Besides clinical symptoms, the most reliable laboratory markers in establishing diagnosis is currently the combined measurement of CRP and a cytokine (IL-6 and IL-8). Due to their different kinetics, a diagnostic gap might occur and thus withholding antimicrobial therapy in clinical suspicion of infection is not acceptable. We therefore need parameters which unerringly differentiate between infants in need for antimicrobial therapy and those who are not. Flow cytometry promises to be a useful tool in this field, allowing the determination of different cellular, dissolved, and functional pathophysiological components of sepsis. Despite technical and methodical advances in flow cytometry, its use in clinical routine is still limited. Advantages and disadvantages of promising new parameters in diagnosis of sepsis performed by flow cytometry, particularly CD64, HLA-DR, and apoptosis, are reviewed here. The necessity of tests to be used as an “ideal” parameter is presented.
FDG-PET for assessment of early treatment response after four cycles of chemotherapy in patients with advanced-stage Hodgkin's lymphoma has a high negative predictive value.

BACKGROUND As positron emission tomography (PET) seems to be a powerful prognostic marker in the treatment of Hodgkin's lymphoma (HL), we analysed the prognostic value of PET after four cycles of combination therapy with bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine and prednisone (BEACOPP) in patients with advanced-stage HL. PATIENTS AND METHODS From January 2004 to March 2007, 50 patients with newly diagnosed HL in clinical stages IIB with large mediastinal mass or extranodal disease, III and IV were treated according to the HD15 protocol of the German Hodgkin Study Group. All patients received a PET scan after four cycles of BEACOPP (PET-4). RESULTS Of the overall group, 14 of 50 patients had a positive PET-4 while 36 had a negative PET-4. At a median observation time of 25 months, 2 of the 14 patients with a positive PET-4 had progressed or relapsed, while there was no progression or relapse in PET-4-negative patients. CONCLUSION Our results indicate a very good negative predictive value of PET-4 in advanced-stage HL patients treated with BEACOPP.
Forage quantity and quality of dual-purpose wheat: changes during grazing and implications for livestock production

Industry benchmarks for ewes grazing pasture recommend a minimum of 1200 kg green DM/ha for late-pregnant twinbearing ewes grazing pastures (Hatcher 2006). The aboveground biomass, or feed on offer (FOO), of wheat crops was 552 and 1092 kg DM/ha at the commencement of grazing by ewes in two experiments in southern NSW (McGrath et al. 2015), and we have now observed ewes safely graze pastures with a mean starting FOO of 330 kg DM/ha (McGrath et al, this issue). The availability of pasture for prehension is a function of both herbage weight and height (Smith et al. 1972), and pasture availability below requirements can have important implications including reduced colostrum production, loss of ewe weight and low lamb birth and growth rates (Penning et al. 1991; Morris and Kenyon 2004; Kenyon et al. 2005), and under-nutrition in late pregnancy can increase the risk of perinatal lamb losses (Kenyon and Webby 2007). Poor nutrition in late-pregnant ewes can also precipitate pregnancy toxaemia (Mavrogianni and Brozos 2008). Ewes did not lose condition and no cases of pregnancy toxaemia were observed in the experiments of McGrath et al. (2015), suggesting ewes were able to meet intake requirements at the low FOO levels used in these experiments.
A cost evaluation of treatment alternatives for mild‐to‐moderate bleeding episodes in patients with haemophilia and inhibitors in Brazil

Summary. The first‐line treatment for mild‐to‐moderate bleeding episodes in patients with haemophilia and inhibitors in Brazil is currently activated prothrombin complex concentrate (aPCC), with recombinant activated factor VII (rFVIIa) used as second‐line therapy or as a last resort. The aim of this study was to determine the cost and effectiveness of these treatments from the perspective of the Brazilian National Health Service. A decision analysis model was constructed to assess total direct medical costs (including drug costs, costs of outpatient or inpatient care, ambulance transportation and cost of concomitant medications) of first‐line treatment with aPCC or rFVIIa. Clinical outcome and resource utilization data were obtained both retrospectively and prospectively and validated by the consensus of an expert panel of Brazilian haematologists. A total of 103 bleeds in 25 patients were included in the analysis. rFVIIa resolved bleeds more quickly (4.4 h) than aPCC (62.6 h) and was more effective (100% vs. 56.7% respectively). Mean total direct medical costs (from initiation to cessation of bleed) were estimated to be US$13 500 (aPCC) and US$7590 (rFVIIa). Extensive sensitivity analyses confirmed the cost‐effectiveness of rFVIIa. Compared with aPCC, rFVIIa was more effective and less expensive when used as first‐line treatment for mild‐to‐moderate bleeding episodes in patients with haemophilia and inhibitors in Brazil. rFVIIa should be considered a first‐line treatment for the management of these patients.
The Evolution of a Business Process Theory - the Case of a Multi-Grounded Theory

In the information systems field there is a great need of different theories. Theory development can be performed in different ways – deductively and/or inductively. Different approaches with their pros and cons for theory development exists. A combined approach, which builds on inductive as well as deductive thinking, has been put forward – a Multi-Grounded Theory approach. In this paper the evolution of a business process theory is regarded as the development of a multi-grounded theory. This evolution is based on empirical studies, the creation of conceptual cohesion as well as a dialectic approach to develop a theoretical synthesis based on antagonistic theories. The result of this process was a multi-grounded business process theory. Multi-grounded means that the theory is empirically, internally and theoretically founded. This business process theory can be used as an aid for business modellers to direct attention towards relevant aspects when business process determination is performed.
Regulation of Porin-Mediated Outer Membrane Permeability by Nutrient Limitation in Escherichia coli

ABSTRACT OmpF and OmpC porins were differentially regulated by nutrient limitation and growth rate in glucose- or nitrogen-limited chemostat cultures of Escherichia coli. Transcriptional and translational ompF fusions showed a sharp peak of expression under glucose limitation at D = 0.3 h−1, with lower amounts at lower and higher growth rates. The peak of OmpR-dependent transcriptional stimulation ofompF under glucose limitation in minimal salts media was about 20-fold above nutrient excess levels and 3-fold higher than that achieved with low osmolarity. Analysis of outer membrane protein levels and results of growth competition experiments with porin mutants were consistent with the enhanced role of OmpF under glucose limitation, but not N limitation. In contrast, OmpC was the major porin under N limitation but was increasingly expressed under glucose limitation at very low growth rates approaching starvation, when OmpF was downregulated. In summary, outer membrane permeability under N-limited, sugar-rich conditions is largely based on OmpC, whereas porin activity is a complex, highly sensitive function of OmpF, OmpC, and LamB glycoporin expression under different levels of glucose limitation. Indeed, the OmpF level was more responsive to nutrient limitation than to medium osmolarity and suggested a significant additional layer of control over the porin-regulatory network.
Pharmacological characterization of glycine-gated chloride currents recorded in rat hippocampal slices.

An inhibitory role for strychnine-sensitive glycine-gated chloride channels (GlyRs) in mature hippocampus has been overlooked, largely due to the misconception that GlyR expression ceases early during development and to few functional studies demonstrating their presence. As a result, little is known regarding the physiological and pharmacological properties of native GlyRs expressed by hippocampal neurons. In this study, we used pharmacological tools and whole cell patch-clamp recordings of CA1 pyramidal cells and interneurons in acutely prepared hippocampal slices from 3- to 4-wk old rats to characterize these understudied receptors. We show that glycine application to recorded pyramidal cells and interneurons elicited strychnine-sensitive chloride-mediated currents (I(gly)) that did not completely desensitize in the continued presence of agonist but reached a steady state at 45-60% of the peak amplitude. Additionally, the inhibitory amino acid, taurine, which has been shown to activate GlyRs in other systems, activated GlyRs expressed by both pyramidal cells and interneurons, although with much less potency than glycine, having an EC(50) 10-fold higher. To examine the potential subunit composition of hippocampal GlyRs, we tested the effect of the GABA(A) receptor antagonist, picrotoxin, on I(gly) recorded from both cell types. At low micromolar concentrations of picrotoxin (< or =100 microM), which selectively block alpha homomeric GlyRs, I(gly) was partially attenuated in both cell types, indicating that alpha homomeric receptors are expressed by pyramidal cells and interneurons. At picrotoxin concentrations < or =1 mM, approximately 10-20% of the whole cell current remained, suggesting that alphabeta heteromeric GlyRs are also expressed because this subtype of GlyR is relatively resistant to picrotoxin antagonism. Finally, we examined whether hippocampal GlyRs are modulated by zinc. Consistent with previous reports in other preparations, zinc elicited a bidirectional modulation of GlyRs, with physiological zinc concentrations (1-100 microM) increasing whole cell currents and concentrations >100 microM depressing them. Furthermore, the same concentration of zinc that potentiates I(gly) suppressed currents mediated by the N-methyl-D-aspartate subtype of the glutamate receptor. Thus we provide a pharmacological characterization of native GlyRs expressed by both major neuron types in hippocampus and show that these receptors can be activated by taurine, an amino acid that is highly concentrated in hippocampus. Furthermore, our data suggest that at least two GlyR subtypes are present in hippocampus and that GlyR-mediated currents can be potentiated by zinc at concentrations that suppress glutamate-mediated excitability.
Annotation Schemes and their Influence on Parsing Results

Most of the work on treebank-based statistical parsing exclusively uses the Wall-Street-Journal part of the Penn treebank for evaluation purposes. Due to the presence of this quasi-standard, the question of to which degree parsing results depend on the properties of treebanks was often ignored. In this paper, we use two similar German treebanks, TuBa-D/Z and NeGra, and investigate the role that different annotation decisions play for parsing. For these purposes, we approximate the two treebanks by gradually taking out or inserting the corresponding annotation components and test the performance of a standard PCFG parser on all treebank versions. Our results give an indication of which structures are favorable for parsing and which ones are not.
The Growth of Dunes in Rivers

Dune response to variable flow has been well documented, but there is no universal model to predict dune dimensions as they respond to imposed flows. Here we use a series of flume experiments to explore dune growth in response to constant flow to better understand the form of dune growth curves. Observations of dune growth from a flat sand bed were made at three flow depths, under five different constant transport stages in a laboratory flume. The transport stages ranged from the sediment entrainment threshold to suspension conditions. The bed was flattened before each run and topography was continually mapped, providing observations of dune growth and morphology at each distinct transport stage condition. The results show that dune growth curves exhibited three different behaviors: (1) exponential growth; (2) punctuated growth, when a period of initially linear growth was abruptly interrupted by exponential growth; and (3) instantaneous growth, when bed evolution happened so quickly that we were unable to take measurements of the phenomenon. Growth behavior is dependent on the applied transport stage, and the time for a growing dune field to reach equilibrium decreases nonlinearly with transport stage. Observations of evolving dunes and the time required to achieve an equilibrium bed state are used to propose a series of relations that can predict dune dimensions through time.
Simultaneous measurement of kynurenine and tryptophan in human plasma and supernatants of cultured human cells by HPLC with coulometric detection.

l-Tryptophan (Trp) is an essential amino acid and an abundant protein component. Trp is metabolized in mammals via two pathways: biosynthesis of the neurotransmitter serotonin and the kynurenine (Kyn) pathway (1)(2). Trp is the substrate for the first step in both of these pathways. In the Kyn pathway, the indole ring of Trp can be opened by the enzymes tryptophan pyrrolase \[tryptophan 2,3-dioxygenase and indoleamine 2,3-dioxygenase (IDO)\] (3). The reactions catalyzed by both of these enzymes constitute the rate-limiting step in the Kyn metabolic pathway (4). The organ distribution of the two enzymes differs, allowing them to be clearly distinguished (5)(6). Tryptophan 2,3-dioxygenase is located primarily in the liver, and its activity is up-regulated in response to Trp and metabolic steroids. IDO can be found in various cells, but it is not active in healthy humans and its activity is induced only during immune responses mediated by proinflammatory cytokines such interferon-γ (7)(8). The enzymatic reactions of the Kyn pathway produce NAD and other intermediates, including Kyn and quinolinic acid (5)(9). The removal of Trp from the microenvironment via this pathway protects the organism by limiting the growth of intracellular pathogens and malignant cells and may also prevent maternal immune reactions against the fetus during pregnancy (10)(11)(12)(13)(14). The Kyn-to-Trp ratio provides an estimate of IDO activity that is independent of baseline Trp concentrations (15)(16)(17). In plasma, Kyn/Trp may be correlated with the concentrations of inflammatory markers, such as neopterin, to ensure that Trp degradation is induced by interferon-γ and involves IDO (18). Kyn/Trp is higher in individuals with diseases that involve an activated cellular immune response or those undergoing cytokine immunotherapy (16)(17)(19). Here we …
Antigen persistence and the control of local T cell memory by migrant respiratory dendritic cells after acute virus infection

Acute viral infections induce robust adaptive immune responses resulting in virus clearance. Recent evidence suggests that there may be depots of viral antigen that persist in draining lymph nodes (DLNs) after virus clearance and could, therefore, affect the adaptive immune response and memory T cell formation. The nature of these residual antigen depots, the mechanism of antigen persistence, and the impact of the persistent antigen on memory T cells remain ill defined. Using a mouse model of influenza virus infection of the respiratory tract, we identified respiratory dendritic cells (RDCs) as essential for both sampling and presenting residual viral antigen. RDCs in the previously infected lung capture residual viral antigen deposited in an irradiation-resistant cell type. RDCs then transport the viral antigen to the LNs draining the site of infection, where they present the antigen to T cells. Lastly, we document preferential localization of memory T cells to the DLNs after virus clearance as a consequence of presentation of residual viral antigen by the migrant RDC.
Fully automatic segmentation of the brain in MRI

A robust fully automatic method for segmenting the brain from head magnetic resonance (MR) images has been developed, which works even in the presence of radio frequency (RF) inhomogeneities. It has been successful in segmenting the brain in every slice from head images acquired from several different MRI scanners, using different-resolution images and different echo sequences. The method uses an integrated approach which employs image processing techniques based on anisotropic filters and "snakes" contouring techniques, and a priori knowledge, which is used to remove the eyes, which are tricky to remove based on image intensity alone. It is a multistage process, involving first removal of the background noise leaving a head mask, then finding a rough outline of the brain, then refinement of the rough brain outline to a final mask. The paper describes the main features of the method, and gives results for some brain studies.
Achalasia - An Update

Achalasia is an esophageal motility disorder of unknown cause, characterized by aperistalsis of the esophageal body and impaired lower esophageal sphincter relaxation. Patients present at all ages, primarily with dysphagia for solids/liquids and bland regurgitation. The diagnosis is suggested by barium esophagram and confirmed by esophageal manometry. Achalasia cannot be cured. Instead, our goal is to relieve symptoms, improve esophageal emptying and prevent the development of megaesophagus. The most successful therapies are pneumatic dilation and surgical myotomy. The overall success rate of graded pneumatic dilation is 78%, with women and older patients responding best. Laparoscopic myotomy, usually combined with a partial fundoplication, has an overall success rate of 87%. Young patients, especially men, are the best candidates for surgical myotomy. Botulinum toxin injection into the lower esophageal sphincter and smooth muscle relaxants are usually reserved for older patients or those with co-morbid illness. The prognosis for achalasia patients to return to near normal swallowing is good, but the disease is rarely "cured" with a single procedure and intermittent touch-up procedures may be required.
Radioprotective Effect of Melatonin on Radiation-Induced Lung Injury and Lipid Peroxidation in Rats

Objective Free radicals generated by ionizing radiation attack various cellular components such as lipids. The lung is a very radiosensitive organ and its damage is a doselimiting factor in radiotherapy treatments. Melatonin (MLT), the major product of the pineal gland acts as a radioprotective agent. This study aims to investigate the radioprotective effects of MLT on malondialdehyde (MDA) levels and histopathological changes in irradiated lungs. Materials and Methods In this experimental study, a total of 62 rats were divided into five groups. Group 1 received no MLT and radiation (unT), group 2 received oral MLT (oM), group 3 received oral MLT and their thoracic areas were irradiated with 18 Gy (oMR), group 4 received MLT by intraperitoneal (i.p.) injection and their thoracic areas were irradiated with 18 Gy (ipM-R), group 5 received only 18 Gy radiation in the thoracic area (R). Following radiotherapy, half of the animals in each group were sacrificed at 48 hours for evaluation of lipid peroxidation and early phase lung injuries. Other animals were sacrificed in the eighth week of the experiment for evaluation of the presence of late phase radiation induced lung injuries. Results Pre-treatment of rats with either i.p injection (p<0.05) and oral administration of MLT (p<0.001) significantly reduced MDA levels in red blood cell (RBC) samples compared to the R group. Furthermore, i.p. injection of MLT decreased MDA levels in plasma and tissue (p<0.05). In the early phase of lung injury, both administration of MLT significantly increased lymphocyte (p<0.05) and macrophage frequency (p<0.001). MLT reduced the lung injury index in the lungs compared to the R group (p<0.05). Conclusion The result of this study confirms the radioprotective effect of MLT on lipid peroxidation, and in both early and late phases of radiation induced lung injuries in an animal model.
Detection of the Antiviral Drug Oseltamivir in Aquatic Environments

Oseltamivir (Tamiflu®) is the most important antiviral drug available and a cornerstone in the defence against a future influenza pandemic. Recent publications have shown that the active metabolite, oseltamivir carboxylate (OC), is not degraded in sewage treatment plants and is also persistent in aquatic environments. This implies that OC will be present in aquatic environments in areas where oseltamivir is prescribed to patients for therapeutic use. The country where oseltamivir is used most is Japan, where it is used to treat seasonal flu. We measured the levels of OC in water samples from the Yodo River system in the Kyoto and Osaka prefectures, Japan, taken before and during the flu-season 2007/8. No OC was detected before the flu-season but 2–58 ng L−1 was detected in the samples taken during the flu season. This study shows, for the first time, that low levels of oseltamivir can be found in the aquatic environment. Therefore the natural reservoir of influenza virus, dabbling ducks, is exposed to oseltamivir, which could promote the evolution of viral resistance.