Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria.

Cyanobacteria have developed an effective photosynthetic CO2 concentrating mechanism (CCM) for improving the efficiency of carboxylation by a relatively inefficient Rubisco. The development of this CCM was presumably in response to the decline in atmospheric CO2 levels and rising O2, both of which were triggered by the development of oxygenic photosynthesis by cyanobacteria themselves. In the past few years there has been a rapid expansion in our understanding of the mechanism and genes responsible for the CCM. In addition, there has been a recent expansion in the availability of complete cyanobacterial genomes, thus increasing our potential to examine questions regarding both the evolution and diversity of components of the CCM across cyanobacteria. This paper considers various CCM and photosynthesis gene components across eight cyanobacteria where significant genomic information is available. Significant conclusions from our analysis of the distribution of various genes indicated the following. Firstly, cyanobacteria have developed with two types of carboxysomes, and this is correlated with the form of Rubisco present. We have coined the terms α-cyanobacteria to refer to cyanobacteria containing Form 1A Rubisco and α-carboxysomes, and β-cyanobacteria having Form 1B Rubisco and β-carboxysomes. Secondly, there are two NDH-1 CO2 uptake systems distributed variably, withProchlorococcus marinus species appearing to lack this CO2 uptake system. There are at least two HCO3- transport systems distributed variably, with some α-cyanobacteria having an absence of systems identified in β-cyanobacteria. Finally, there are multiple forms of carbonic anhydrases (CAs), but with only β-carboxysomal CA having a clearly shown role at present. The α-cyanobacteria appear to lack a clearly identifiable carboxysomal CA. A pathway for the evolution of cyanobacterial CCMs is proposed. The acquisition of carboxysomes triggered by the rapid decline of atmospheric CO2 in the Phanerozoic is argued to be the initial step. This would then be followed by the development of NDH-1 CO2-uptake systems, followed by the development of low-and high-affinity HCO3- transporters. An intriguing question is, were carboxysomes developed first in cyanobacteria, or did they originate by the lateral transfer of pre-existing proteobacterial bacterial microcompartment genes? The potentially late evolution of the CCM genes in cyanobacteria argues for a polyphyletic and separate evolution of CCMs in cyanobacteria, algae, and higher plants.
Does synovigeny confer reproductive plasticity upon a parasitoid wasp that is faced with variability in habitat richness

Understanding the factors that constrain the reproductive success of animals and their demographics requires detailed insight into the processes of resource acquisition and allocation in relation to habitat richness. Parasitoid wasp females are valuable models in this respect because their lifetime reproductive success is closely tied to host availability. Parasitoids that manufacture eggs throughout adult life (i.e. ‘synovigenic’ species) and characteristically acquire nutrients via feeding are predicted to be plastic in their allocation to egg manufacture. Using the synovigenic parasitoid wasp Venturia canescens, we tested whether this prediction holds when females are faced with variation in the availability of both hosts and food. Laboratory experiments were conducted to determine how environmental variation affects parasitoid reproductive success and the lifetime dynamics of egg load and of major nutrient types. Our results, surprisingly, show that female V. canescens lacks a significant degree of reproductive plasticity under our experimental conditions. In particular, allocation of resources to reproduction was high irrespective of host availability. We attribute this lack of flexibility to the low energy content of V. canescens' eggs and to features peculiar to the ecology of this species. Our findings shed new light on the physiological factors that constrain parasitoid lifetime reproductive success.
Swath grazing potential of spring cereals, field pea and mixtures with other species

There is little information on the relative suitability of cereal species and field pea or their mixtures for winter swath grazing. The objective of this study was to compare the swath grazing potential of small-grain cereal and field pea (Pisum sativa L.) monocultures, their mixtures, and mixtures with other species, by evaluating forage yield in the fall and changes in nutritive value due to weathering from fall until spring. The monocultures and mixtures were seeded in early summer and swathed in late September with conventional farm equipment for 3 yr. Dry matter yield was measured by harvesting a subplot (1.22 × 3.62 m) across each plot prior to swathing. A cross-section sample of swath was taken for quality determination immediately after swathing, in late November and April. In vitro digestible organic matter (IVDOM), protein, and neutral (NDF) and acid detergent fiber (ADF) concentrations were measured for each sampling time. Generally, barley (Hordeum vulgare L.), oat (Avena sativa L.) and field .
A Comparative Study to access the Stress and Coping Strategiesamong Gastrointestinal Cancer Patients and Non- Cancerous Chronic Gastrointestinal Disease Patients

Background:Improved diagnosis and treatment methods, increasing incidence rates and prolonged life expectancy have steadily increased the number of people living with cancer diagnosis. Objectives:The objective of the study was to assess and compare the level of stress and coping strategies adopted by gastrointestinal cancer patients with other non-cancerous chronic gastrointestinal disease patients at selected hospital, New Delhi, in view to develop an educational pamphlet. Methods:This descriptive comparative study was conducted in oncology day care and OPD of Institute of Liver and Biliary Sciences, New Delhi. Total 200 patients (100 GI cancer patients and 100 other non-cancerous chronic GI disease patients) were selected using convenience sampling technique and matched for age and gender. Perceived Stress Scale and Brief COPE was used to collect data regarding stress and coping strategies among GI cancer patients and other non-cancerous chronic GI disease patients. Data was analyzed using descriptive and inferential statistics. Results:Study findings shows significant higher proportion of GI cancer patients (64%) had stress as compared to other non cancerous chronic GI patients (5%). Problem focused coping strategies were most used by GI cancer patients and other non-cancerous chronic GI disease patients. Emotion focused coping strategies was significantly (r = 0.267, p= 0.007) correlated with stress in other non-cancerous chronic GI Disease Patients. Conclusion:On the basis of study findings, it is concluded that GI cancer patients had high stress. The study helped in identifying psychological needs of the patients and the educational pamphlet aided the patients to reduce the stress and adopt an effective coping strategies.
Social alienation caused by precocious puberty and hypothalamic obesity in patients with suprasellar arachnoid cysts - Case studies and literature review of a rare but significant disorder

Suprasellar arachnoid cysts (SAC), due to their location, are a separate group, regarding clinical symptoms and therapeutic approach, compared to AC in other locations. For this reason they are more similar to other benign suprasellar lesions. SACs are most often diagnosed in children. Symptoms of SAC depend on the age in which they occurred. The treatment needs the engagement of consultant doctors from many fields: neurosurgery, neurology, ophthalmology, endocrinology and radiology and should be also supported by psychologists. *Correspondence to: Agata Halabuda, Polish – American Institute of Pediatrics / Jagiellonian University Kraków, Poland, E-mail: agatahalabuda@gazeta.pl
Evaluating the physiological and physical consequences of capture on post‐release survivorship in large pelagic fishes

Sharks, tunas and billfishes are fished extensively throughout the world. Domestic and international management measures (quotas, minimum sizes, bag limits) mandate release of a large, yet poorly quantified, number of these fishes annually. Post-release survivorship is difficult to evaluate, because standard methods are not applicable to large oceanic fishes. This paper presents information on the current approaches to characterising capture stress and survivorship in sharks, tunas and marlins. To assess mortality associated with capture stress, researchers must examine the cumulative impacts of physical trauma and physiological stress. Physical trauma, manifested as external and internal tissue and organ damage, is caused by fishing gear and handling. Gross examination and histopathological sampling have been used to assess physical trauma and to infer post-release survivorship. Exhaustive anaerobic muscular activity and time out of water cause physiological stress, which has been quantified in these fishes through the analyses of blood chemistry. Conventional, acoustic and archival tagging have been used to assess post-release survivorship in these species. Future studies relating capture stress and post-release survivorship could yield information that helps fishermen increase survivorship when practicing catch and release.
The pathogenesis of olivary changes in clioquinol intoxication

Inferior olivary changes were found in the central nervous system of five patients with subacute myelo‐opticneuropathy induced by long‐term clioquinol administration. The histological findings in the olivary nuclei could not be distinguished from those seen in olivary hypertrophy due to other causes. In two of the five cases, dentate neurons were relatively well preserved. However, there were minor abnormalities in the neuropil of the dentate nuclei and amiculum olivae with loss of myelin and fibrous gliosis. These changes suggested that processes and efferent fibers of the dentato‐olivary system were degenerating and led to speculation that the olivary changes in clioquinol intoxication might be secondary to distal dominant axonopathy in the dentato‐olivary pathway.
AtBXL1 Encodes a Bifunctional b-D-Xylosidase/ a-L-Arabinofuranosidase Required for Pectic Arabinan Modification in Arabidopsis Mucilage

Following pollination, the epidermal cells of the Arabidopsis ( Arabidopsis thaliana ) ovule undergo a complex differentiation process that includes the synthesis and polar secretion of pectinaceous mucilage followed by the production of a secondary cell wall. Wetting of mature seeds leads to the rapid bursting of these mucilage secretory cells to release a hydrophilic gel that surrounds the seed and is believed to aid in seed hydration and germination. A novel mutant is identiﬁed where mucilage release is both patchy and slow and whose seeds display delayed germination. While developmental analysis of mutant seeds reveals no change in mucilage secretory cell morphology, changes in monosaccharide quantities are detected, suggesting the mucilage release defect results from altered mucilage composition. Plasmid rescue and cloning of the mutant locus revealed a T-DNA insertion in AtBXL1 , which encodes a putative bifunctional b - D -xylosidase/ a - L -arabinofuranosidase that has been implicated as a b - D -xylosidase acting during vascular development. Chemical and immunological analyses of mucilage extracted from bxl1 mutant seeds and antibody staining of developing seed coats reveal an increase in (1 / 5)-linked arabinans, suggesting that BXL1 is acting as an a - L -arabinofuranosidase in the seed coat. This implication is supported by the ability to rescue mucilage release through treatment of bxl1 seeds with exogenous a - L -arabinofuranosidases. Together, these results suggest that trimming of rhamnogalacturonan I arabinan side chains is required for correct mucilage release and reveal a new role for BXL1 as an a - L -arabinofuranosidase acting in seed coat development. patchy Mutants Appear to Undergo Normal Seed Coat Development But Have an Altered
Exact and Relaxed Convex Formulations for Shallow Neural Autoregressive Models

Neural networks offer powerful generative capabilities in unsupervised learning tasks. Despite recent empirical success, these models often have complex optimization landscapes, and their theoretical properties are not well understood. To address these issues, we present convex formulations of autoregressive neural models with one hidden layer. Speciﬁcally, we prove an exact equivalence between these models and constrained, regularized logistic regression by using semi-inﬁnite duality to embed the data matrix onto a higher dimensional space and introducing inequality constraints. To make this formulation more tractable, we approximate the constraints using a hinge loss or drop them altogether. Furthermore, we demonstrate faster training and competitive performance of these implementations compared to their neural network counterparts on a variety of data sets. Consequently, we introduce techniques to derive scalable and interpretable models that are equivalent to black box, neural network based autoregressive models.
DESCRIPTION OF A NEW SPECIES OF AKODON (RODENTIA: SIGMODONTINAE) FROM SOUTHERN BRAZIL

Abstract Cranial and external morphology of 54 specimens of rodents of the genus Akodon from southern Brazil was analyzed. The sample included 27 individuals with a karyotype of 2n = 44 and 13 with 2n = 46 and 14 nonkaryotyped animals. Principal components analysis separated individuals with 2n = 44 from those with 2n = 46. Individuals with 2n = 44 were distinguished from those with 2n = 46 by narrow and elongated molars, ectolophid present, narrow interorbital breadth, reduced tegmen tympani, and distal baculum with the central and lateral digit approximately equal in size and proportions, not enlarged in the extremity. Discriminant functions analyses including 6 A. sanctipaulensis individuals and holotypes of A. serrensis and A. s. leucogula resulted in 3 distinct groups. The 2n = 46 individuals were related to A. serrensis, but those with 2n = 44 were not assignable to any described species for Akodon. We describe and propose the recognition of a new species for the genus.
Palaeoclimatic models help to understand current distribution of Caucasian forest species

Spatial and temporal constraints on dispersal explain the absence of species from areas with potentially suitable conditions. Previous studies have shown that post-glacial recolonization has shaped the current ranges of many species, yet it is not completely clear to what extent interspecific differences in range size depend on different dispersal rates. The inferred boundaries of glacial refugia are difficult to validate, and may bias spatial distribution models (SDMs) that consider post-glacial dispersal constraints. We predicted the current distribution of 12 Caucasian forest plants and animals, factoring in the effective geographical distance from inferred glacial refugia as an additional predictor. To infer glacial refugia, we tested the transferability of the current SDMs based on the distribution of climatic variables, and projected the most transferable ones onto two climate scenarios simulated for the Last Glacial Maximum (LGM). We then calculated least-cost distances from the inferred refugia, using elevation as a friction surface, and recalculated the current SDMs incorporating the distances as an additional variable. We compared the predictive powers of the initial with the final SDMs. The palaeoclimatic simulation that best matched the distribution of species was assumed to represent the closest fit to the true palaeoclimate. SDMs incorporating refugial distance performed significantly better for all but one studied species, and the Model for Interdisciplinary Research on Climate (MIROC) climatic simulation provided a more convincing pattern of the LGM climate than the Community Climate System Model (CCSM) simulation. Our results suggest that the projection of suitable habitat models onto past climatic conditions may yield realistic boundaries of glacial refugia, and that the current distribution of forest species in the study region is strongly associated with locations of former refugia. We inferred six major forest refugia throughout western Asia: (1) Colchis; (2) western Anatolia; (3) western Taurus; (4) the upper reaches of the Tigris River; (5) the Levant; and (6) the southern Caspian basin. The boundaries of the modelled refugia were substantially broader than the refugia boundaries inferred solely from pollen records. Thus, our method could be used to: (1) improve models of current species distributions by considering the dispersal histories of the species; and (2) validate alternative reconstructions of palaeoclimate with current distribution data. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 231‐248. ADDITIONAL KEYWORDS: forests ‐ fuzzy envelopes ‐ Mahalanobis distance ‐ post-glacial dispersal ‐ range modelling ‐ reconstruction of palaeoclimate ‐ variable selection ‐ western Asia.
Debugging the performance of Maven’s test isolation: experience report

Testing is the most common approach used in industry for checking software correctness. Developers frequently practice reliable testing-executing individual tests in isolation from each other-to avoid test failures caused by test-order dependencies and shared state pollution (e.g., when tests mutate static fields). A common way of doing this is by running each test as a separate process. Unfortunately, this is known to introduce substantial overhead. This experience report describes our efforts to better understand the sources of this overhead and to create a system to confirm the minimal overhead possible. We found that different build systems use different mechanisms for communicating between these multiple processes, and that because of this design decision, running tests with some build systems could be faster than with others. Through this inquiry we discovered a significant performance bug in Apache Maven’s test running code, which slowed down test execution by on average 350 milliseconds per-test when compared to a competing build system, Ant. When used for testing real projects, this can result in a significant reduction in testing time. We submitted a patch for this bug which has been integrated into the Apache Maven build system, and describe our ongoing efforts to improve Maven’s test execution tooling.
Adoption and Challenges of Mobile Banking Systems in Ethiopia: Adoption and Challenges of Mobile Banking Systems in Ethiopia: The Case of Cooperative Bank of Oromiya The Case of Cooperative Bank of Oromiya

The incorporation of information system into organizations for the purpose of getting competitive advantage, easing workload, providing intangible (soft) work place and coping up with technological advancement has become an indispensable for organizations. Due to these many companies (like banks) are getting advantages of information communication technology implementation like Mobile Banking (M-banking), Internet banking, Automatic Teller Machine, etc. Accordingly Ethiopian commercial banks have implemented M-banking system into their service system. This research examine adoption of M-banking system in Ethiopia focusing on Cooperative bank of Oromiya with respect to the challenges which can influence the bank from taking advantage and expected benefits of M-banking system derived by adopting the system. The result of the research indicated that, drivers of M-banking are relative advantage, perceived ease of use and perceived usefulness while challenges are perceived risks, trust reliability and lack of ICT infrastructure.
Genetic and morphologic characterization of four putative cylindrospermopsin producing species of the cyanobacterial genera Anabaena and Aphanizomenon

Cylindrospermopsin (CYN) is a potent hepatotoxic alkaloid that has been detected in freshwater samples worldwide and is produced by a number of cyanobacterial species, mainly of the genera Cylindrospermopsis, Aphanizomenon and Anabaena. Cylindrospermopsis raciborskii is a morphologically distinctive species which forms a genetically well-defined cluster. In contrast, some species within Aphanizomenon and Anabaena are morphologically not clearly assignable to either genera and both genera are polyphyletic. In the Cylindrospermopsis cluster CYN producing and non-producing strains co-occur, but it is not known if GYM producing and non-producing strains are closely related in Anabaena and Aphanizomenon. Here we attempt to disentangle the phylogenetic relationships of four taxa of the genera Anabaena and Aphanizomenon, some of which are known as CYN producers. We have sequenced and phylogenetically analysed partial sequences of the 16S rRNA gene, cpcBA-IGS and rpoCI from 31 cyanobacteria isolates of the genera Aphanizomenon and Anabaena and have documented morphotypic characteristics of new and recently isolated strains. Our results do not corroborate the separation of Aph. gracile and Aph. flos-aquae into separate species. In contrast, they support the distinction of Ana. bergii and Aph. ovalisporum into distinct taxa. Further, Ana. bergii is most likely not a CYN producing species.
Iberian Baetic Endemic Flora and the Implications for a Conservation Policy

The Baetic ranges in the Iberian Peninsula are extremely rich and outstanding in biological terms. Based on the existing literature, herbarium sheets and our own field research, we provide a checklist of the endemic flora growing in the Baetic chorological province. The checklist includes 418 taxa belonging to 43 families, with the species pool concentrated within large families. The highest number of endemic species is recorded in the altitudinal range of 1300–1500 m a.s. l. Hemicryptophytes represent the most frequent life form (45.5%). Conservation priorities should concentrate on non-woody life forms (particularly on hemicryptophytes), and on high mountain areas. Most of the taxa can be ascribed to serial shrublands (36.87%), or rock- or scree-dwelling formations (26.25%), with climactic forest formations playing a minor role (3.24%). This successional position has important implications for conservation programmes. Therefore, a clear distinction should be made between serial or plagioclimactic formations (e.g. dolomite thyme-scrub communities) and degraded communities of little interest for the preservation of biodiversity (e.g. synanthropic vegetation). Astragalus nevadensis subsp. andresmolinae (Díez-Garretas & Asensi) Mota & F.J. Pérez-García is proposed as a new combination.
The Hylland-Zeckhauser Rule Under Bi-Valued Utilities

The Hylland-Zeckhauser (HZ) rule is a well-known rule for probabilistic assignment of items. The complexity of the rule has received renewed interest recently with Vazirani and Yannakakis (2020) proposing a strongly polynomial-time algorithm for the rule under bi-valued utilities, and making several general insights. We study the rule under the case of agents having bi-valued utilities. We point out several characterizations of the HZ rule, drawing clearer relations with several well-known rules in the literature. As a consequence, we point out alternative strongly polynomial-time algorithms for the HZ solution. We also give reductions from computing the HZ solution to computing well-known solutions based on leximin or Nash social welfare. An interesting contrast is that the HZ rule is group-strategyproof whereas the unconstrained competitive equilibrium with equal incomes rule is not even strategyproof. We also clarify which results change when moving from 1-0 binary utilities to the more general bi-valued utilities.