Miracle-dz/UniFAR-FTUs huggingface dataset:
Biker’s Dilemma: Cooperation between Foes

Cooperative behavior is subject to exploitation by individuals that are unwilling to share resources or efforts. Evolu- tion of social behavior by individual selection is therefore difficult to achieve. The study of simple symmetric two-player games of cooperation and defection suggest ways to circumvent this difficulty, the game of Prisoner™s Dilemma in particular. This game has nevertheless failed to explain recently reported social behavior among lions with persistent differences in willingness to cooperate among individuals. We propose and analyze a slightly differ- ent game, Biker™s Dilemma, that describes the observed behavior and predicts the variation seen in the lion popula- tion.
Focal Loss Function based DeepLabv3+ for Pathological Lymph Node Segmentation on PET/CT

Pathological lymph node segmentation plays an important role in clinical practice. Yet it is still a challenging problem owing to low contrast to surrounding structures. In this paper, we take a deep learning based approach for pathological lymph node segmentation task. Semantic segmentation architecture, DeepLabv3+, which has the advantage to segment objects in a multi-scale way, is adopted in this paper. Meanwhile, the focal loss function, which originally applied in object detection task to deal with the imbalance class number, is integrated into DeepLabv3+ architecture for the imbalance of voxel class between pathological lymph nodes and background. Compared to the cross entropy loss function and dice function, the focal loss function can improve the segmentation performance in terms of sensitivity and dice in the DeepLabv3+ segmentation architecture. Four-fold cross validation has been done on 63 volumes containing 214 malignant lymph nodes and the mean sensitivity of 87% and average Dice score of 75% are obtained for pathological lymph node segmentation.
1H NMR-Based Metabolomics Coupled With Molecular Docking Reveal the Anti-Diabetic Effects and Potential Active Components of Berberis vernae on Type 2 Diabetic Rats

The dried stem bark of Berberis vernae C.K. Schneid. , known as “Xiao-bo-pi” in Chinese, is a representative anti-diabetic herb in traditional Tibetan medical system. However, its anti-diabetic mechanisms and active components remain unclear. In this study, 1H NMR-based metabolomics, biochemistry assay, molecular docking, and network analysis were integrated to evaluate the anti-diabetic effects of B. vernae extract on type 2 diabetic rats, and to explore its active components and underlying mechanisms. Diabetes was induced by high-fat diet and streptozotocin. After 30 days of treatment, B. vernae extract significantly decreased the serum levels of fasting blood glucose, insulin, insulin resistance index, glycated serum protein, TNF-α, IL-1β, and IL-6, whereas significantly increased the serum levels of insulin sensitivity index in type 2 diabetic rats. A total of 28 endogenous metabolites were identified by 1H NMR-based metabolomics, of which 9 metabolites that were changed by diabetes were significantly reversed by B. vernae extract. The constructed compound-protein-metabolite-disease (CPMD) interaction network revealed the correlation between chemical constituents, target proteins, differential metabolites, and type 2 diabetes. Ferulic acid 4-O-β-D-glucopyranoside, bufotenidine, jatrorrhizine, and berberine showed good hit rates for both the 30 disease-related proteins and 14 differential metabolites-related proteins, indicating that these four compounds might be the active ingredients of B. vernae against type 2 diabetes. Moreover, pathway analysis revealed that the anti-diabetic mechanisms of B. vernae might be related to its regulation of several metabolic pathways (e.g., butanoate metabolism) and disease-related signal pathways (e.g., adipocytokine signaling pathway). In summary, B. vernae exerts a significant anti-diabetic effect and has potential as a drug candidate for the treatment of type 2 diabetes.
Factors affecting seasonal variations in demersal fish assemblages at an ecocline in a tropical–subtropical estuary

Seasonal changes of fish species composition in terms of biomass, density and number of species in three areas of the main channel of the Paranagua Estuary (axis east–west) are described in relation to seasonal fluctuations in salinity, water temperature and dissolved oxygen in the main channel. Two hundred and thirty-four samples were collected monthly, between July 2000 and June 2001, in the main channel. Seventy-nine species of 29 families were captured with a total estimated mean density and biomass of 1513 individuals ha−1 and 34 kg ha−1, respectively. The number of species and total mean density differed significantly among areas and seasons, but the total mean biomass differed only significantly throughout the ecocline (areas) of the Paranagua Estuary. For the most abundant species, the mean densities of Stellifer rastrifer, Aspistor luniscutis, Menticirrhus americanus, Sphoeroides testudineus, Cynoscion leiarchus and Symphurus tesselatus (with the exception of Cathorops spixii and Genidens genidens) differed significantly among seasons. The mean biomass of these species, with the exception of G. genidens, S. rastrifer, A. luniscutis and S. testudineus, also differed significantly for the factor seasons. Area was a significant factor for the eight most abundant species (density and biomass), except S. testudineus (density), G. genidens, C. leiarchus and S. tesselatus (biomass). The season v. area interaction term was significant for C. leiarchus (density). Most of these differences occurred during the rainy season when fishes concentrated principally in the middle of the estuary, where the salinity remained stable. It is suggested that the salinity stability in the middle of the estuary is the main reason why the most estuarine resident fish species move downstream and remain there, regardless of the increased freshwater runoff. Moreover, canonical correspondent analysis output detected that during the late rainy season, the variable dissolved oxygen (P < 0·01) was the most important environmental variable, responsible for structuring patterns of fishes assemblages in the west–east axis of Paranagua Estuary. During the end of the dry season, both salinity (P < 0·01) and dissolved oxygen (P < 0·05) were responsible for this ecological feature in the estuary. Finally, it was possible to detect that juveniles and adults of some important species respond differently to seasonal fluctuations of the ecocline-determining environmental factors. This behaviour is suggested as a strategy to avoid competition and predation during the rainy season in the middle estuary. The Paranagua Estuary did not fit with the pre-existing models described in the tropical and subtropical estuarine fish literature since its main channel fish assemblages remained within its bounds even during the rainy season.
Insights Into the Eruptive Dynamics of Small Caldera-Forming Eruptions: The Case Study of the Welded Scoriae of Vulcano (Aeolian Islands, Italy)

A multi-disciplinary study, integrating volcanological field observations, petrography, whole rock geochemistry and textural and compositional analyses on plagioclase crystals has been carried out on the products of Monte Luccia, Spiaggia Lunga, and Quadrara eruptions, occurred between 48 and 21 kyrs on the island of Vulcano. These products are all characterized by welded scoria blankets, and their eruptions have been generally related to the formation and/or re-activation of ring faults bordering the “Il Piano” caldera. The aim of the work is to reconstruct the pre- and syn-eruptive dynamics acting within their magma plumbing systems and the related link with the phases of caldera collapse. At the bottom of the stratigraphic sequences, the presence of base surge deposits suggests that all the eruptions started with a phreatomagmatic phase fed by a shallow reservoir. Textural and microanalytical study of plagioclase crystals of Spiaggia Lunga eruption revealed that the phreatomagmatic event activated the ascent of a volatile-rich, basaltic magma residing at 5–11 km of depth. This basaltic magma mixed with the resident shallow one, and was poured out during the course of the eruption producing a sustained lava-fountaining phase. The subsequent caldera collapse, identified by a layer of chaotic breccia interbedded in the scoriae deposit, has been linked to the partial emptying of the shallow magma reservoir. In contrast to what observed for recent eruptive events at Vulcano, the onset of the magmatic phase would be attributed to a self-activation due to volcano-tectonic events, and not to a pressurization of the plumbing system related to the ascent of deep magma batches. As concerns the Mt. Luccia deposits, bordering the eastern rim of the “Il Piano” caldera, the absence of plagioclase in the mineralogical assemblage suggests the eruption of a deeper magma (>11 km b.s.l.), rapidly ascending through the re-activated ring faults of “Il Piano” caldera. At Quadrara eruption, the occurrence of a layer of white biotite-bearing latitic pumices overlying the basal phreatomagmatic deposits suggests the involvement a shallow, isolated reservoir where the increase of volatile pressure allowed the crystallization of hydrous phases. A deeper shoshonitic magma was involved later in the eruption, forming the welded scoria level at the top of the sequence.
An epidemiological study on effect of air pollutants on respiratory morbidity in adults of a critically polluted city of northern India

Research into the health effects of air pollution is ongoing all over the world. This study aimed to assess the impact of air pollution on the respiratory disease in a critically polluted city of northern India. Air pollution has become a hazardous problem in India with an increase in urbanization, vehicle density and industrial smoke emission. Cross-sectional household survey was conducted in “exposed” and “reference” population. Ambient air quality data were assessed in both towns. Only the level of total suspended particulate matter (TSP) was observed to be more than permissible limit in Mandi Gobindgarh. Results of multivariate logistic regression showed that after controlling the confounding variables, cough (OR = 1.59, 95% CI 1.21-2.12, P = 0.001), phlegm (OR = 1.56, 95% CI 1.17-2.07, P = 0.003), wheeze (OR = 1.50, 95% CI 1.04-2.17, P = 0.03), chronic bronchitis (OR = 2.23, 95% CI 1.10-4.53, P = 0.03) and obstructive defects (OR = 1.86, 95% CI 1.43-2.42, P = 0.001) were significantly higher amongst the residents of Mandi Gobindgarh. Adult population of Mandi Gobindgarh has significantly more chronic respiratory morbidity as compared to that of Morinda. It is concluded that the level of TSP in the ambient air is responsible for the poor respiratory health in adults of Mandi Gobindgarh.
Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.
Expression patterns of AP1, FUL, FT and LEAFY orthologs in Vitaceae support the homology of tendrils and inflorescences throughout the grape family

The leaf‐opposed tendril, a characteristic organ in Vitaceae (grape family), is likely a morphological key innovation for the family. It has been considered as the homologous organ of the inflorescence. Expression of floral related genes has been studied extensively in the model species, grapevine (Vitis vinifera), to uncover molecular mechanisms that determine the development of a common uncommitted primordium (or an anlage) into an inflorescence or a tendril. However, to investigate the homology of tendrils and inflorescences in Vitaceae, evidence only from the highly derived grapevine is insufficient. Therefore, gene sequences of four key floral meristem genes, i.e., FUL, AP1, FT and LEAFY orthologs were obtained from transcriptome data of 14 Vitaceae species, the grapevine genome and the outgroup Leea guineensis. Additionally, expression patterns of these four genes were studied in leaves, tendrils, and inflorescences of five phylogenetically distinct Vitaceae species. Expression of the AP1 ortholog was only detected in the tendril and the inflorescence but not in the leaf for all species, indicating that the tendril is more like the inflorescence than the leaf and that the tendrils from these six species including grapevine are likely homologous. Meanwhile, expression of the LEAFY ortholog was found in the inflorescence but not in the tendril and leaf, suggesting that the LEAFY ortholog expression might play a role in determining whether an anlage develops into a tendril or an inflorescence. Based on combined evidence from the expression patterns of these four genes, the possible mechanisms on the evolution of tendrils are discussed.
Resilience of cereal crops to abiotic stress: A review

In the last century, conventional selection and breeding program proved to be highly effective in improving crops against abiotic stresses. Therefore, breeding for abiotic stress tolerance in crop plants should be given high research priority as abiotic stresses are the main factor negatively affecting crop growth and productivity throughout the globe. Advancement in physiology, genetics and molecular biology, have greatly improved our understanding of plant responses to stresses. Many studies show that salt tolerance is tightly associated with the ability to maintain ion homeostasis under salinity. Na + transporter SKC1 unloads Na + from xylem; plasma membrane N + /H + antiporter SOS 1 excludes sodium out of cytosol, and tonoplast Na + /H + antiporter NHX 1 sequesters Na + into the vacuole. Silicon deposition in exodermis and endodermis of rice root reduces sodium transport through the apoplastic pathway. A number of transcription factors regulate stress-inducible gene expression that leads to initiating stress responses and establishing plant stress tolerance. Over expression of some transcription factors, including DREB/CBF and NAC, enhances salt, drought, and cold tolerance in rice. A variant of one of ERF family genes, Sub1A-1 , confers immersion tolerance to lowland rice. These findings and their exploitation will hold promise for engineering breeding to protect crop plants from certain abiotic stresses. Although, cereal crops are also quite sensitive to various abiotic stresses, hence in this short review, we will present recent progresses in adaptation of cereal crops to salinity, drought and cold tolerance are emphasized and the future potentials are highlighted. Keywords: Cereal crops, abiotic stresses, food insecurity, molecular breeding, quantitative trait loci (QTLs), salinity, water stress. African Journal of Biotechnology , Vol 13(29) 2908-2921
Sacral root afferent nerve signals for a bladder neuroprosthesis

The purpose of this study was to investigate the feasibility of implanting a cuff electrode chronically on the sacral nerve roots for recording of afferent nerve signals. These signals could be used as feedback for an implantable neuroprosthesis to control the overactive bladder. Cuff electrodes were implanted in seven female Göttingen mini pigs on the extradural sacral nerve roots S1 (n=1), S2 (n=4) and S3 (n=3), and connected to a subcutaneously implanted telemetric device. Nerve signals were evoked by electrical stimulation of the clitoral nerve and mechanical stimulation of the relevant dermatome. Nerve signals were recorded in all animals on the day of implantation, and in five animals at the first follow-up experiment, 7 to 19 days after implantation. The most successful implant lasted 383 days. Reasons for terminating an implant were puncture of the skin, infection, suspected brain damage after anesthesia, and no nerve responses. Histological results showed signs of neural damage in 4 of 5 examined animals. The results show that cuff electrodes can be implanted chronically for recording of sacral root afferent nerve signals, but also that when nerve damage is inflicted during implantation or later on, this will be clearly reflected in the recorded nerve signals.
Şehir İçi İkametgâh Hareketliliğine Kuramsal Bir Bakış (A Contextual View to the Intra-Urban Residential Mobility)

<b>Turkish Abstract:</b> ‘Beşeri sermaye yaklaşımı’ göç ya da ikametgâh hareketliliğini, rasyonel karar vermenin ve faydayı en üst düzeye çıkarma sürecinin bir sonucu olarak görmektedir. Neo-klasik ekonomik bir çerçeve içinde ikametgâh hareketliliği, genellikle emek hareketi olarak tanımlanmaktadır. Rossi, ikametgâh hareketliliğinin ailenin yaşam döngüsü değişiklerine eşlik eden ve aile bileşimi değişiklikleri nedeniyle ortaya çıkan konut ihtiyaçlarını karşılamak üzere gerçekleştirdiği düzenleme süreci olduğunu ileri sürmüştür. Göç ve hareketlilik araştırmalarında davranışsal yaklaşıma ilgi, Wolpert’in göç kararında ‘yer yararlılığı’ terimiyle kavramsallaştırdığı teorik bir yazısından sonra artmıştır. Bu terim Wolpert tarafından, bir yerin başka yerlere göre çekicilik veya iticiliklerinin bireysel değerlendirmesi şeklinde tanımlanmıştır. Sosyoloji ve planlama içinde geliştirilen bir başka teorik çerçeve, hareketliliği ev veya bulunduğu semtin özelliklerinden doğan memnuniyetsizliğin bir sonucu olarak görmektedir. Memnuniyetsizlik yaklaşımı literatürü, halen oturulan ikametgâh çevresinin, hane halkının ürettiği baskı veya memnuniyetsizlikle etkileşim halinde olduğu ve bu memnuniyetsizliğin bazı eşiklere ulaştığında hane halkının, ikametgâh hareketine yol açabilecek bir arama sürecine başladığı üzerinde durmaktadır. Bu makale, göç, ikametgâh hareketliliği ve yeniden yerleşme hakkındaki literatürü gözden geçirmekte ve ikametgâh hareketliliği sürecini anlamak üzere bağlamsal bir çerçeve sunmaktadır. <br><br><b>English Abstract:</b> ‘Human capital approach’, considers migration or residential mobility as the result of rational decision making and utility maximisation process. Within a neo-classical economic framework, mobility is described principally as labour movement. Rossi suggested that residential mobility is a process by which families adjust their housing to the housing needs that are generated by the shifts in family composition that accompany life cycle changes. In migration and mobility researches, the interest in the behavioural approach derives largely from a theorical paper by Wolpert, in which the decision to migrate was conceptualized in term of ‘place utility’. As defined by Wolpert, the term refers to an individual’s personal evaluation of the attractiveness or unattractiveness of a location relative to other locations. Another framework that developed in sociology and planning views mobility as an outcome of dissatisfaction with characteristics of the house or neighbourhood. In the literature on dissatisfaction approaches, the current residential environment interacts with the household to produce stress or dissatisfaction and when this dissatisfaction reaches some threshold the household then begins a search process that may lead to a residential move. This paper examines literature about migration, residential mobility, and relocation and presents a contextual framework for understanding the process of residential mobility.
Pharmacological Manipulation of Kv7 Channels as a New Therapeutic Tool for Multiple Brain Disorders

Kv7 (“M-type,” KCNQ) K+ currents, play dominant roles in controlling neuronal excitability. They act as a “brake” against hyperexcitable states in the central and peripheral nervous systems. Pharmacological augmentation of M current has been developed for controlling epileptic seizures, although current pharmacological tools are uneven in practical usefulness. Lately, however, M-current “opener” compounds have been suggested to be efficacious in preventing brain damage after multiple types of insults/diseases, such as stroke, traumatic brain injury, drug addiction and mood disorders. In this review, we will discuss what is known to date on these efforts and identify gaps in our knowledge regarding the link between M current and therapeutic potential for these disorders. We will outline the preclinical experiments that are yet to be performed to demonstrate the likelihood of success of this approach in human trials. Finally, we also address multiple pharmacological tools available to manipulate different Kv7 subunits and the relevant evidence for translational application in the clinical use for disorders of the central nervous system and multiple types of brain insults. We feel there to be great potential for manipulation of Kv7 channels as a novel therapeutic mode of intervention in the clinic, and that the paucity of existing therapies obligates us to perform further research, so that patients can soon benefit from such therapeutic approaches.