bluuebunny/crossref_metadata_2025 huggingface dataset:
Espacios urbanos fosilizados en Oviedo
Authors: Obeso Muñiz Ícaro
Published: December 2023

En el contexto de los procesos urbanos de las ciudades medias españolas tras la crisis de 2008 esta investigación se aproxima a las consecuencias que la paralización del proceso urbanizador tiene en el paisaje urbano. Para ello se toma como caso de estudio la ciudad de Oviedo en la que convergen varios procesos que pueden resultar de interés para el resto de las ciudades y para futuras investigaciones de síntesis sobre los procesos urbanos contemporáneos. Por un lado, se observa la existencia de enclaves dentro del tejido urbano que tras la pérdida de su función no han encontrado alternativas y se ven afectadas por el abandono. Por otro, las consecuencias de un planeamiento urbanístico estrechamente vinculado a los ciclos alcistas de la economía han producido que la expansión prevista mediante la clasificación de ámbitos de suelo urbanizable no haya sido efectiva. De tal modo, tanto en la ciudad consolidada como en su periferia se observen situaciones de parálisis, falta de expectativas o proyectos inconclusos que en alguno de los casos superan la década. Así pues, estos espacios urbanos fosilizados parecen enclaves ajenos a su entorno y mientras la futura regeneración llega se ven expuestos a un intenso proceso de degradación.
Simposio de ciudades medias y pequeñas españolas en UNED Tudela (Dos ediciones, 2022-2023)
Authors: Cepeda García Emilio Jesús
Published: December 2023

El Centro Asociado de la UNED en Tudela ha organizado un simposio sobre ciudades medias y pequeñas españolas en respuesta a la creciente demanda de foros de debate sobre este tema. La iniciativa busca abordar la situación actual de estas ciudades desde un enfoque multidisciplinar, y está dirigida a responsables municipales, profesionales en disciplinas urbanas y estudiantes. El simposio tiene como objetivo reflexionar y proponer soluciones para valorar y considerar estos territorios, a menudo subestimados.
 
Se centra en aquellas ciudades con una población entre 20 y 300 mil habitantes, capitales de provincia y cabeceras comarcales, incluso ciudades satélites de áreas metropolitanas. Todas ellas conforman esa España «en la que nunca pasa nada», lejos de los grandes focos mediáticos, centrados en la España vaciada.
 
La primera edición se celebró en noviembre de 2022, e incluyó debates y conferencias sobre la definición y situación actual de estas ciudades. La segunda, en octubre de 2023, llevó por lema "Territorio, identidad y arraigo", abordando procesos y transformaciones recientes y las ventajas y valores de estas ciudades.
Informe editorial 2023
Authors: Montagud Mayor Xavier
Published: December 2023

Informe editorial TERRA 2023
The servants of the Muslim cult of the Tobolsk province in the late 1890s – 1920s.
Authors: Fajzullina Guzel Chakhvarovna
Published: December 2023

The subject of the study is information about the servants of the Muslim cult of the Tobolsk province in the late 90s of the XIX century - the 20s of the XX century, contained in various archival sources: Muslim metric books in the Old Tatar language, the First general census of the Russian Empire in 1897, documents (charter, protocols of the founders, lists of members and inventory of property Mohammedan religious communities, an agreement on the use of a Mohammedan liturgical building, minutes of general meetings, lists of parishioners, etc.) of Mohammedan religious communities for the 20s (Ishtama yurts, Komarov yurts, Medyan yurts, Mirim Yurts, Sabanak yurts, Sauskansky yurts, Suklem yurts, Escalba yurts). The purpose of the research is to study the composition of the Islamic clergy by introducing little-studied sources into scientific circulation. When studying the composition of the servants of the Muslim cult of the Tobolsk province in the late 1890s - 1920s, such scientific methods as historiographical analysis, comparative historical method, and source analysis were used. The novelty of the research is seen in the involvement of poorly studied sources in Russian and Tatar languages and in the systematization of disparate materials about Muslim clerics according to the chronological principle. An analysis of archival documents on the servants of the Muslim cult of the Tobolsk province in the late 1890s - 1920s showed that priests previously approved in the spiritual rank continued to serve in the Mohammedan religious communities organized in the early 1920s. Moreover, in the early years of Soviet power (up to 1925), new persons were appointed to various positions – imam, imam-khatib, mugallim, mullah, muezzin. It has been established that in the Soviet period, continuity in the service of a religious cult by blood relationship continues to be traced. Some ministers of the cult did not cease to indicate their ethnic origin, namely Bukhara. The author has revealed variability in the spelling of personal names of priests, which is associated with the formation of linguistic norms concerning the spelling of anthroponyms of the Tatar population: fused, separate, semi-alphabetic (hyphenated).
Modelling Driver Behaviour at Urban Signalised Intersections Using Logistic Regression and Machine Learning
Authors: Alomari Ahmad H. , AL-Mistarehi Bara’ W. , Al-Jammal Al-Jammal A. , Alhadidi Taqwa I. , Obeidat Motasem S.
Published: December 2023

This study investigated several factors that may influence driver actions throughout the yellow interval at urban signalised intersections. The selected samples include 2,168 observations. Almost 33% of drivers stopped ahead of the stop line, 60% passed the intersection through the yellow interval, and 7% passed after the yellow interval was complete (red light running, RLR violations). Binary logistic regression models showed that the chance of passing went up as vehicle speed went up and down as the gap between the vehicle and the traffic light and green interval went up. The movement type and vehicle position influenced the passing probability, but the vehicle type did not. Moreover, multinomial logistic regression models showed that the legal passing probability declined with the growth in the green time and vehicle distance to the traffic signal. It also increased with the growth in the speed of approaching vehicles. Also, movement type directly affected the chance of legally passing, but vehicle position and type did not. Furthermore, the driver’s performance during the yellow phase was studied using the k-nearest neighbours algorithm (KNN), support vector machines (SVM), random forest (RF) and AdaBoost machine learning techniques. The driver’s action run prediction was the most accurate, and the run-on-red camera was the least accurate.
Optimising Traffic Safety – Locating Traffic Gendarmes Based on Multi-Criteria Decision Making
Authors: Abdulvahitoğlu Adnan , Vural Danışment , Abdulvahitoğlu Aslı
Published: December 2023

Turkey’s expanding population and growing economy have resulted in a significant increase in automobile ownership, leading to a rise in traffic volume and, subsequently, an increase in the number of accidents. The increase in the number of deaths and injuries caused by traffic accidents has motivated authorities and automobile manufacturers to work together to mitigate the impact of traffic accidents. Therefore, the demand for better roads, modern technologies and higher-quality driver training is becoming increasingly urgent for traffic safety. Due to the scale of harm to the country’s economy and society caused by the material and moral losses, resulting from traffic accidents, traffic safety and management is one of the most important government initiatives. One of the responsible units of traffic safety and management in Turkey is the traffic gendarme. This study reviewed the categories of traffic accidents, the number of accidents, and the road network that occurred in a province's gendarme responsibility area in Turkey and linked them with the number of traffic gendarmes in that province. Thus, the study utilised mixed integer programming based on multi-criteria decision-making methods to identify the areas where these traffic gendarmes will be deployed according to established principles.
Influence of Traffic Flow and Meteorological Conditions on Air Pollution – A Case Study
Authors: Simeunović Milja , Kojić Radoslav , Ralević Nebojša , Pitka Pavle , Kovačević Tatjana
Published: December 2023

In this paper, the influence of traffic flow volume and meteorological conditions on carbon monoxide (CO), particulate matter (PM), ozone (O3) and sulphur dioxide (SO2) concertation is determined based on the measurements conducted at a selected location over a 784-hour period. Multivariate Analysis of Variance (MANOVA) and Analysis of Variance (ANOVA) were applied to the data set. Regression analysis was also used to determine trends in pollutant concentrations as a function of traffic flow and meteorological parameters. Analysis of the obtained data indicates a statistically significant relationship between traffic volume and meteorological parameters on the one hand and pollutants on the other. However, increase in the value of certain input variables does not necessarily result in the increase in pollutant concentration. CO and O3 showed a significant dependence on the number of vehicles, while for SO2 the influence of commercial vehicles was greater than that of passenger cars. The relationship between the number of vehicles and PM was not evident at the study site.
Old Latin bouerum and Iouerum from a Diachronic Point of View
Authors: Witczak Krzysztof
Published: December 2023

Abstract The aim of this article is to discuss two Old Latin aberrant genitive plural forms in -erum, namely bouerum «bouum» (Cato, Agr. 62) or Iouerum «Iouum» (Varro, Ling. VIII 74), on the basis of the morphological and semantic considerations. It is hard to imagine how the regular third declension forms bouum and Iouum could be changed into bouerum and Iouerum. In his commented edition of Varro’s De lingua Latina (2019) Wolfgang de Melo, following Roland Kent, explains them as «analogical formations», influenced by iu – ge˘ rum n. «an acre; jugerum (of land)» (→ bo˘ ue˘ rum) and gen. pl. Ve˘ne˘ rum «of statues of Venus» (→ Io˘ ue˘ rum). This explanation should be rejected for at least two reasons: semantic and morphological. The innovative genitive plural in -e–rum, I will argue, was based on old nominative and accusative dual forms with additional plural morphology: cf. *boue– nom.-acc. du. «two oxen», gen. pl. boue–rum «of oxen» (originally «of two oxen»), *Ioue– «two Jupiters» (here in elliptic use: «Jupiter and Juno»), gen. pl. Ioue–rum «of Jupiters» (originally «of two Jupiters; i.e., Jupiter and Juno»).
Sexual coordination in a whole-brain map of prairie vole pair bonding
Authors: Gustison Morgan L. , Muñoz-Castañeda Rodrigo , Osten Pavel , Phelps Steven M.
Published: December 2023

Sexual bonds are central to the social lives of many species, including humans, and monogamous prairie voles have become the predominant model for investigating such attachments. We developed an automated whole-brain mapping pipeline to identify brain circuits underlying pair-bonding behavior. We identified bonding-related c-Fos induction in 68 brain regions clustered in seven major brain-wide neuronal circuits. These circuits include known regulators of bonding, such as the bed nucleus of the stria terminalis, paraventricular hypothalamus, ventral pallidum, and prefrontal cortex. They also include brain regions previously unknown to shape bonding, such as ventromedial hypothalamus, medial preoptic area and the medial amygdala, but that play essential roles in bonding-relevant processes, such as sexual behavior, social reward and territorial aggression. Contrary to some hypotheses, we found that circuits active during mating and bonding were largely sexually monomorphic. Moreover, c-Fos induction across regions was strikingly consistent between members of a pair, with activity best predicted by rates of ejaculation. A novel cluster of regions centered in the amygdala remained coordinated after bonds had formed, suggesting novel substrates for bond maintenance. Our tools and results provide an unprecedented resource for elucidating the networks that translate sexual experience into an enduring bond.
A computational model predicts sex-specific responses to calcium channel blockers in mesenteric vascular smooth muscle
Authors: Hernandez-Hernandez Gonzalo , O’Dwyer Samantha C. , Matsumoto Collin , Tieu Mindy , Fong Zhihui , Yang Pei-Chi , Lewis Timothy J. , Santana L. Fernando , Clancy Colleen E.
Published: December 2023

The function of the smooth muscle cells lining the walls of systemic arteries and arterioles is to regulate the diameter of the vessels to control blood flow and blood pressure. Here, we describe an
in-silico
model, which we call the “Hernandez-Hernandez model”, of electrical and Ca
2+
signaling in arterial myocytes based on new experimental data indicating sex-specific differences in male and female arterial myocytes from resistance arteries. The model suggests the fundamental ionic mechanisms underlying membrane potential and intracellular Ca
2+
signaling during the development of myogenic tone in arterial blood vessels. Although experimental data suggest that K
V
1.5 channel currents have similar amplitudes, kinetics, and voltage dependencies in male and female myocytes, simulations suggest that the K
V
1.5 current is the dominant current regulating membrane potential in male myocytes. In female cells, which have larger K
V
2.1 channel expression and longer time constants for activation than male myocytes, predictions from simulated female myocytes suggest that K
V
2.1 plays a primary role in the control of membrane potential. Over the physiological range of membrane potentials, the gating of a small number of voltage-gated K
+
channels and L-type Ca
2+
channels are predicted to drive sex-specific differences in intracellular Ca
2+
and excitability. We also show that in an idealized computational model of a vessel, female arterial smooth muscle exhibits heightened sensitivity to commonly used Ca
2+
channel blockers compared to male. In summary, we present a new model framework to investigate the potential sex-specific impact of anti-hypertensive drugs.
Reduced discrimination between signals of danger and safety but not overgeneralization is linked to exposure to childhood adversity in healthy adults
Authors: Klingelhöfer-Jens Maren , Hutterer Katharina , Schiele Miriam A. , Leehr Elisabeth , Schümann Dirk , Rosenkranz Karoline , Böhnlein Joscha , Repple Jonathan , Deckert Jürgen , Domschke Katharina , Dannlowski Udo , Lueken Ulrike , Reif Andreas , Romanos Marcel , Zwanzger Peter , Pauli Paul , Gamer Matthias , Lonsdorf Tina B.
Published: December 2023

Exposure to adverse childhood experiences (ACEs) is a strong predictor for developing behavioral, somatic and psychopathological conditions. Exposure to threat-related early adversity has been suggested to be specifically linked to altered emotional learning as well as changes in neural circuits involved in emotional responding and fear. Learning mechanisms are particularly interesting as they are central mechanisms through which environmental inputs shape emotional and cognitive processes and ultimately behavior. Multiple theories on the mechanisms underlying this association have been suggested which, however, differ in the operationalization of ACEs. 1,402 physically and mentally healthy participants underwent a fear conditioning paradigm including a fear acquisition and generalization phase while skin conductance responses (SCRs) and different subjective ratings were acquired. ACEs were retrospectively assessed through the childhood trauma questionnaire and participants were assigned to individuals exposed or unexposed to at least moderate adverse childhood experiences according to established cut-off criteria. In addition, we provide exploratory analyses aiming to shed light on different theoretical accounts on how ACE’s impact individual risk profiles (i.e., cumulative risk account, specificity model, dimensional model). During fear acquisition training and generalization, we observed reduced discrimination in SCRs between the CS+ and the CS-, primarily due to reduced CS+ responding in exposed individuals. During fear generalization, no differences in generalization gradients were observed between exposed and unexposed individuals but generally blunted physiological responses in exposed individuals. No differences between the groups were observed in ratings in any of the experimental phases. The lower CS discrimination in SCRs in exposed individuals was evident across operationalizations according to the cumulative risk account, specificity as well as dimensional model. However, none of these theories showed clear explanatory superiority. Our results stand in stark contrast to typical patterns observed in patients suffering from anxiety and stress-related disorders (i.e., reduced CS discrimination due to increased responses to safety signals). Thus, reduced CS+ responding in individuals exposed to ACEs, yet not showing signs of psychopathology, may represent a specific characteristic of this resilient subgroup that warrants further investigation with respect to its relation to risk and resilience. In addition, we conclude that theories linking ACEs to psychopathology need refinement.
Homeostatic regulation of rapid eye movement sleep by the preoptic area of the hypothalamus
Authors: Maurer John J , Lin Alexandra , Jin Xi , Hong Jiso , Sathi Nicholas , Cardis Romain , Osorio-Forero Alejandro , Lüthi Anita , Weber Franz , Chung Shinjae
Published: December 2023

Rapid eye movement sleep (REMs) is characterized by activated electroencephalogram (EEG) and muscle atonia, accompanied by vivid dreams. REMs is homeostatically regulated, ensuring that any loss of REMs is compensated by a subsequent increase in its amount. However, the neural mechanisms underlying the homeostatic control of REMs are largely unknown. Here, we show that GABAergic neurons in the preoptic area of the hypothalamus projecting to the tuberomammillary nucleus (POAGAD2→TMN neurons) are crucial for the homeostatic regulation of REMs in mice. POAGAD2→TMN neurons are most active during REMs, and inhibiting them specifically decreases REMs. REMs restriction leads to an increased number and amplitude of calcium transients in POAGAD2→TMN neurons, reflecting the accumulation of REMs pressure. Inhibiting POAGAD2→TMN neurons during REMs restriction blocked the subsequent rebound of REMs. Our findings reveal a hypothalamic circuit whose activity mirrors the buildup of homeostatic REMs pressure during restriction and that is required for the ensuing rebound in REMs.
Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species
Authors: Li Xueyou , Bleisch William V , Hu Wenqiang , Li Quan , Wang Hongjiao , Chen Zhongzheng , Bai Ru , Jiang Xue-Long
Published: December 2023

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here, we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalayas to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87%) and human presence (83%) compared to those located in habitats with lower human modification (64%) and human presence (65%) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance, corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences.
Human disturbance increases spatiotemporal associations among mountain forest terrestrial mammal species
Authors: Li Xueyou , Bleisch William V. , Hu Wenqiang , Li Quan , Wang Hongjiao , Chen Zhongzheng , Bai Ru , Jiang Xuelong
Published: December 2023

Spatial and temporal associations between sympatric species underpin biotic interactions, structure ecological assemblages, and sustain ecosystem functioning and stability. However, the resilience of interspecific spatiotemporal associations to human activity remains poorly understood, particularly in mountain forests where anthropogenic impacts are often pervasive. Here we applied context-dependent Joint Species Distribution Models to a systematic camera-trap survey dataset from a global biodiversity hotspot in eastern Himalaya to understand how prominent human activities in mountain forests influence species associations within terrestrial mammal communities. We categorized anthropogenic pressures into chronic human modification and acute direct human presence and compared their effects on spatiotemporal associations among species. We obtained 10,388 independent detections of 17 focal species (12 carnivores and five ungulates) from 322 stations over 43,163 camera days of effort. We identified a higher incidence of positive associations in habitats with higher levels of human modification (87 %) and human presence (83 %) compared to those located in habitats with lower human modification (64 %) and human presence (65 %) levels. We also detected a significant reduction of pairwise encounter time at increasing levels of human disturbance (human modification: mean = −1.07, 95% CI = −1.39 to −0.73; human presence: mean = −0.69, 95% CI = −0.92 to −0.46), corresponding to more frequent encounters between pairs of species. Our findings indicate that human activities can push mammals together into more frequent encounters and associations, which likely influences the coexistence and persistence of wildlife, with potential far-ranging ecological consequences. With increasing human presence and human modification of areas throughout the world, identifying thresholds of anthropogenic activity that shift species relationships, limiting human activity and increasing landscape connectivity across protected areas may be imperative to maintain interspecific spatiotemporal associations that underpin ecosystem resilience.
Predicting the effect of CRISPR-Cas9-based epigenome editing
Authors: Batra Sanjit Singh , Cabrera Alan , Spence Jeffrey P. , Hilton Isaac B. , Song Yun S.
Published: December 2023

Epigenetic regulation orchestrates mammalian transcription, but functional links between them remain elusive. To tackle this problem, we here use epigenomic and transcriptomic data from 13 ENCODE cell types to train machine learning models to predict gene expression from histone post-translational modifications (PTMs), achieving transcriptome-wide correlations of ∼ 0.70 − 0.79 for most samples. In addition to recapitulating known associations between histone PTMs and expression patterns, our models predict that acetylation of histone subunit H3 lysine residue 27 (H3K27ac) near the transcription start site (TSS) significantly increases expression levels. To validate this prediction experimentally and investigate how engineered vs. natural deposition of H3K27ac might differentially affect expression, we apply the synthetic dCas9-p300 histone acetyltransferase system to 8 genes in the HEK293T cell line. Further, to facilitate model building, we perform MNase-seq to map genome-wide nucleosome occupancy levels in HEK293T. We observe that our models perform well in accurately ranking relative fold changes among genes in response to the dCas9-p300 system; however, their ability to rank fold changes within individual genes is noticeably diminished compared to predicting expression across cell types from their native epigenetic signatures. Our findings highlight the need for more comprehensive genome-scale epigenome editing datasets, better understanding of the actual modifications made by epigenome editing tools, and improved causal models that transfer better from endogenous cellular measurements to perturbation experiments. Together these improvements would facilitate the ability to understand and predictably control the dynamic human epigenome with consequences for human health.
Soybean RIN4 represents a mechanistic link between plant immune and symbiotic signaling
Authors: Tóth Katalin , Kim Daewon , Cho Sung-Hwan , Nguyen Cuong T. , Nguyen Tran H. N. , Hartanto Christopher , Michno Jean-Michel , Stec Adrian O. , Stupar Robert M. , Stacey Gary
Published: December 2023

The legume-rhizobium symbiosis represents a unique and beneficial interaction between legumes and nitrogen-fixing soil bacteria, called rhizobia. The initiation and development of this symbiosis is complex and begins with recognition of key molecular signals, produced by the plant and its symbiont, which determine symbiotic compatibility. Current data suggest that the invading symbiont initially triggers plant immune responses that are subsequently suppressed. Hence, there is growing evidence that features of plant immunity may be relevant to symbiotic establishment. RIN4 is a key immune regulator in plants, regulating basal immunity and it is also targeted by pathogen effector proteins that either confer susceptibility or resistance, depending on the presence of the appropriate resistance protein. Surprisingly, we found that RIN4 was rapidly phosphorylated upon rhizobial inoculation of soybean root hairs. RNAi silencing and mutant studies indicate that RIN4 expression is essential for effective nodulation of soybean. RIN4 phosphorylation occurs within a fifteen amino acid motif, which is highly conserved within the Fabales (legumes) and Rosales orders, that comprise species capable of nitrogen-fixing endosymbiosis with rhizobia. RIN4 proteins mutated in this conserved phosphorylation site failed to support efficient soybean nodulation. Phosphorylation of this site is mediated by the symbiotic receptor-like kinase, SymRK, a well-studied member of the symbiotic signaling pathway. The data implicate RIN4 phosphorylation as a key mediator of rhizobial compatibility, interconnecting symbiotic and immune signaling pathways.The nitrogen fixing legume-rhizobium symbiosis is a cornerstone of sustainable agriculture, with ongoing efforts to transfer this unique ability to non-leguminous crop plants. Plants are surrounded by a myriad of microbes in the soil, and, therefore, require constant surveillance in order to distinguish between a pathogen or symbiont. Plants monitor for specific molecular signals that indicate pathogen or symbiont presence. We show that RIN4, a key immune regulator, plays an essential role in promoting the development of the symbiotic nitrogen-fixing relationship between soybean and its compatible symbiont
Bradyrhizobium japonicum
. Therefore, RIN4 is likely a key player in mediating the appropriate response upon infection by friend or foe.
Bacterial vampirism mediated through taxis to serum
Authors: Glenn Siena J , Gentry-Lear Zealon , Shavlik Michael , Harms Michael J , Asaki Thomas J , Baylink Arden
Published: December 2023

Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remain poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized an injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce bacterial attraction to the serum source. This response is orchestrated through chemotaxis and the chemoattractant L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. We find Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provide a competitive advantage for migration into enterohemorrhagic lesions. We define this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients as ‘bacterial vampirism’, which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.
Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration
Authors: Jensen Mathias Fynbo , Nielsen Morten
Published: December 2023

Predicting the interaction between Major Histocompatibility Complex (MHC) class I-presented peptides and T-cell receptors (TCR) holds significant implications for vaccine development, cancer treatment, and autoimmune disease therapies. However, limited paired-chain TCR data, skewed towards well-studied epitopes, hampers the development of pan-specific machine-learning (ML) models. Leveraging a larger peptide-TCR dataset, we explore various alterations to the ML architectures and training strategies to address data imbalance. This leads to an overall improved performance, particularly for peptides with scant TCR data. However, challenges persist for unseen peptides, especially those distant from training examples. We demonstrate that such ML models can be used to detect potential outliers, which when removed from training, leads to augmented performance. Integrating pan-specific and peptide-specific models alongside with similarity-based predictions, further improves the overall performance, especially when a low false positive rate is desirable. In the context of the IMMREP22 benchmark, this modeling framework attained state-of-the-art performance. Moreover, combining these strategies results in acceptable predictive accuracy for peptides characterized with as little as 15 positive TCRs. This observation places great promise on rapidly expanding the peptide covering of the current models for predicting TCR specificity. The NetTCR 2.2 model incorporating these advances is available on GitHub (https://github.com/mnielLab/NetTCR-2.2) and as a web server at https://services.healthtech.dtu.dk/services/NetTCR-2.2/.
On Nirmala Indices of Some Hex-derived Networks of Type Three and Their Subdivision Networks
Authors:   Department of Mathematics, Institute of Science, Banaras Hindu University, Varanasi - 221005, Uttar Pradesh, India, Rai Shikha , Das Shibsankar ,   Department of Mathematics, Institute of Science, Banaras Hindu University, Varanasi - 221005, Uttar Pradesh, India
Published: December 2023

Several degree-based topological indices have a vital role in the inspection of the chemical properties of various chemical networks. Hex-derived networks, made up of hexagonal mesh networks, have wide applications in the fields of technology, pharmacy and physical sciences. In this research work, we focus on different hex-derived networks of the third type of dimension n and their subdivisions. The Nirmala indices (such as the Nirmala index, the first inverse Nirmala index and the second inverse Nirmala index) are newly introduced degree-based topological indices. Here, we compute the values of these Nirmala indices for the above networks under consideration by operating their standard mathematical formulas and the M-polynomial based method. In addition, we plot the Nirmala indices of the networks and their subdivisions in different dimensions for the purpose of comparative studies among them. The results acquired are helpful in demonstrating the structural properties of considered hex-derived networks and their subdivisions. Also, it may influence the researchers for comparative based studies of the structure and their subdivisions in the sense of the Nirmala indices.
Describing Weighted Safety with Weighted LTL over Product omega-valuation Monoids
Authors:   Department of Mathematics of the Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece, Mandrali Eleni
Published: December 2023

We define the notion of k-safe infinitary series over idempotent ordered totally generalized product omega-valuation monoids that satisfy specific properties. For each element k of the underlying structure (different from the neutral elements of the additive, and the multiplicative operation) we determine two syntactic fragments of the weighted LTL with the property that the semantics of the formulas in these fragments are k-safe infinitary series. For specific idempotent ordered totally generalized product omega-valuation monoids we provide algorithms that given a weighted Buchi automaton and a weighted LTL formula in these fragments, decide whether the behavior of the automaton coincides with the semantics of the formula.
Shedding light on the Ophel biome: the trans-Tethyan phylogeography of the sulfide shrimp Tethysbaena (Peracarida: Thermosbaenacea) in the Levant
Authors: Guy-Haim Tamar , Kolodny Oren , Frumkin Amos , Achituv Yair , Velasquez Ximena , Morov Arseniy R.
Published: December 2023

Background

Tethysbaena are small peracarid crustaceans inhabiting extreme environments such as subterranean lakes and thermal springs, represented by endemic species found around the ancient Tethys, including the Mediterranean, Arabian Sea, Mid-East Atlantic, and the Caribbean Sea. Two Tethysbaena species are known from the Levant: T. relicta, found along the Dead Sea-Jordan Rift Valley, and T. ophelicola, found in the Ayyalon cave complex in the Israeli coastal plain, both belonging to the same species-group based on morphological cladistics. Along the biospeleological research of the Levantine subterranean fauna, three biogeographic hypotheses determining their origins were proposed: (1) Pliocenic transgression, (2) Mid-late Miocenic transgression, and (3) The Ophel Paradigm, according to which these are inhabitants of a chemosynthetic biome as old as the Cambrian.

Methods

Tethysbaena specimens of the two Levantine species were collected from subterranean groundwaters. We used the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear ribosomal 28S (28S rRNA) gene to establish the phylogeny of the Levantine Tethysbaena species, and applied a molecular clock approach for inferring their divergence times.

Results

Contrary to the morphological cladistic-based classification, we found that T. relicta shares an ancestor with Tethysbaena species from Oman and the Dominican Republic, whereas the circum-Mediterranean species (including T. ophelicola) share another ancestor. The mean age of the node linking T. relicta from the Dead Sea-Jordan Rift Valley and Tethysbaena from Oman was 20.13 MYA. The mean estimate for the divergence of T. ophelicola from the Mediterranean Tethysbaena clade dated to 9.46 MYA.

Conclusions

Our results indicate a two-stage colonization of Tethysbaena in the Levant: a late Oligocene transgression, through a marine gulf extending from the Arabian Sea, leading to the colonization of T. relicta in the Dead Sea-Jordan Rift Valley, whereas T. ophelicola, originating from the Mesogean ancestor, inhabited anchialine caves in the coastal plain of Israel during the Mid-Miocene.
Género, afrontamiento diádico y síntomas depresivos en personas chilenas en relación de pareja
Authors:   , Espinosa Díaz William Segundo
Published: December 2023

La depresión es uno de los trastornos de salud mental cuya prevalencia se ha exacerbado en mayor medida durante los últimos años. Estudios realizados en Chile muestran la alta presencia de sintomatología depresiva en la población general y en especial entre las mujeres. La teoría interpersonal de la depresión de Coyne propone que las personas con síntomas depresivos se involucran en comportamientos interpersonales desadaptativos que, aunque tienen la intención de aliviar la angustia, alejan los apoyos sociales y aumentan los síntomas depresivos. De esta manera es que se configura un escenario donde las personas pueden afectar el bienestar de su pareja, provocando malestar y angustia la cual en muchos casos debe ser atendida por el sistema de salud. Para entender como las parejas tratan de afrontar la diversidad de estresores, entre ellos las enfermedades es que Bodenmann ha propuesto el Modelo Sistémico Transaccional de Afrontamiento del Estrés. Este modelo conceptualiza a la pareja como un sistema el cual formula estrategias sean positivas, negativas o comunes a fin de combatir el estrés interno o externo que los aqueja. Al relacionar el afrontamiento diádico con la depresión se ha encontrado un número muy limitado de investigaciones que se enfoquen en este ámbito, sobre todo a nivel de población latinoamericana. La evidencia actual sostiene que un mejor afrontamiento diádico se correlaciona con una disminución en la sintomatología depresiva sin embargo al considerar el factor de género no existe evidencia concluyente sobre el rol moderador que esta variable puede desempeñar. El objetivo de esta investigación es establecer la relación del género con el afrontamiento diádico y la sintomatología depresiva en personas que se encuentran en una relación de pareja. El estudio es de tipo cuantitativo, no experimental, transversal, de tipo descriptivo, comparativo y correlacional, enmarcado en el proyecto Fondecyt 1220824 de mayor extensión. La muestra del estudio consideró 354 personas quienes completaron un cuestionario autoadministrado aplicado en forma virtual. Los instrumentos aquí considerados incluyen datos demográficos, la evaluación de la depresión mediante el test Patient Health Questionnarie (PHQ 9) y la evaluación del Afrontamiento diádico del Estrés, mediante el test (Dyadic Coping Inventory; Bodenmann, 2008). Para el análisis de datos se usó el software estadístico R Studio en su versión 2023.06.2. Los resultados sugieren que el género no cumple con un rol moderador entre el afrontamiento diádico y la sintomatología depresiva. Por otro lado, se encontró que el afrontamiento diádico tiene un efecto significativamente negativo en la puntuación de la sintomatología depresiva independientemente del género. Estos resultados constituyen un aporte sobre cómo las parejas pueden contribuir a la disminución o al aumento de la sintomatología depresiva tanto a nivel de paciente como en la diada y las implicancias clínicas a considerar para el tratamiento efectivo de la depresión.
Material de psicoeducación para promover la adherencia al tratamiento en pacientes que presentan uveítis de la Unidad de Oftalmología del Hospital Clínico Universidad de Chile
Authors:   , Molina Moya María Ignacia
Published: December 2023

Introducción: La uveítis es una inflamación del tracto uveal, reduce la visión y puede producir una pérdida visual severa. Afecta principalmente a adultos en edad productiva, generando impactos sociales, económicos y psicológicos. La reducción en la visión, desconocimiento de la enfermedad, complejidad del tratamiento y efectos secundarios, son factores que producen malestar psicológico, afectando la adherencia al tratamiento. Objetivo: Diseñar material de psicoeducación que contribuya a mejorar la adherencia al tratamiento en pacientes que presentan uveítis de la Unidad de Oftalmología del Hospital Clínico Universidad de Chile. Métodos: El presente proyecto sigue un diseño cualitativo, donde se recopiló, analizó e integró información a partir de entrevistas a distintos agentes clave que contribuyeron al diseño del material, que luego fue evaluado por expertos y pacientes. Resultados: Las entrevistas revelan un impacto psicológico y en su funcionalidad. El limitado conocimiento sobre ésta y los efectos secundarios del tratamiento explican en parte este malestar. Conclusiones: El material diseñado aborda las preocupaciones de los pacientes y familiares, y elementos consistentes con el modelo COM-B que contribuyen a mejorar la adherencia al tratamiento. Por lo tanto, el modelo permite diseñar la estrategia y también comprender lo que le ocurre a los pacientes y familiares.
The good and the better, sampling tropical intertidal rock pool fishes: a comparison between visual census vs. rock pool bailing method
Authors: González-Murcia Saúl , Alvarado-Larios Raquel , Guerra Jennifer , Logan Murray
Published: December 2023

Numerous sampling methods have been applied to study intertidal rock pool fishes. There is limited information comparing the performance and suitability of such methods, which complicates comparisons between studies. We compared the performance of the bailing and visual census methods in 10 rock pools to quantify abundance, species richness, and structure of fish assemblages in rock pool intertidal systems considering fish residency affinities, rock pool volume, and substratum rugosity. Sampling was conducted 13 times across the complete set of 10 rock pools from June to December, 2018. Each of the pools was sampled with a visual census and then the bailing method. A sampling event was defined as the process of conducting both a visual and a bailing survey in a single rock pool. In total, 1,749 individuals of 14 species were detected using the bailing method, whereas 438 individuals of 8 species were recorded via visual census. The bailing method yielded higher abundance and species richness of resident, opportunist, and transient fish than the visual census. The detection of individuals and species showed a positive association with rock pool volume and negative association with substratum rugosity for both methods. In 32 sampling events, the bailing method detected fish correcting reports of fish absence (false negatives) recorded with the visual census. For the bailing method, resident fishes dominated the fish assemblage, whereas, for the visual census, resident and opportunist fishes contributed similarly to the community.
Metinden Görüntü Üretme Potansiyeli Olan Yapay Zekâ Sistemleri Sanat ve Tasarım Performanslarının İncelenmesi
Authors: ASLAN Tamer , AYDIN Kemal
Published: December 2023

2022 yılının son çeyreğinde popülerliği artan yapay zekâ tabanlı görsel üretimlerin sanat eseri niteliğine sahip olup olamayacağı veya dijital sanat kapsamında değerlendirilip değerlendirilemeyeceği tartışmaları gündemde giderek daha çok yer almakta ve popülaritesini artırmaktadır. Yapay zekâ algoritmaları her ne kadar dijital çağın sanatsal bir içeriği olarak uzun yıllardır yeni medya çalışmalarında kullanılmaktadır. Ancak yapay zekânın giderek gelişen içeriğiyle ulaşılan son noktada, yazılım bilgisine sahip olmanın gerekliliği ortadan kalkmış, ilgili programlar herkesin rahatlıkla erişim sağlayıp kullanabileceği seviyeye gelmiştir. Metinden görüntü üreten yapay zekâ sistemleri, yapay zekânın temelini oluşturan makine öğrenme (machine learning, ML) teknolojileriyle birlikte çeşitli internet sitelerinden toplanan görsel ve yazınsal veri kümelerinden yararlanmakta ve kişinin yazacağı komut doğrultusunda daha önce ‘hiç var olmamış’ görseller oluşturabilmektedir. İstem olarak adlandırılan metin girdisi görüntü oluşumunda büyük rol oynamakta, yazılan her kelime farklı parametreleri değiştirerek yapay zekânın izleyeceği yolu belirlemektedir. Bu görsel çıktı, programa girilen her sözcük ile birlikte değişmekte ufak ayrıntılar bile sonuçta büyük farklılıklar oluşturabilmektedir. Geçmişte sanat eğitimi almamış veya hiçbir sanatsal faaliyette bulunmamış kişilerin yapay zekâya “eser” ürettirebilmesi, güncel sanatın ve sanatçının konumu ile alakalı soru işaretleri yaratmaktadır. Yapay zekâ-insan etkileşimi neticesinde, deneysel ve yinelemeli bir süreçten geçerek gerçekleştirilen üretimlerin sanatsal boyutlarına dair incelemelerin yapılması önemli görülmektedir. Bu araştırmada, nitel araştırma yöntemi/örnek olay incelemesiyle metinden görüntü üreten yapay zekâ sistemleri kullanılarak sanatsal bir çıktının elde edilebilirliği ve kimlerin, hangi süreçler doğrultusunda bu çıktıya ulaşabileceği sorularına cevap aranmıştır.
A Cross-sectional Study on Microbiological Patterns Associated with Urinary Tract Infections in Hospitalised Women: Analysis of Their Antimicrobial Sensitivity and Clinical Risk Factors
Authors: Sharma Disha , Sharma Divya
Published: December 2023

Introduction: Urinary Tract Infections (UTIs) are one of the most common infections, with a predominance in females. To overcome the menace of antibiotic resistance in UTIs, it is important to delineate and follow the local antibiotic resistance patterns of these pathogens. This helps in formulating institutional infection control policies and providing guidance for antibiotic therapy. Knowledge of risk factors for UTIs in hospitalised patients is used to formulate preventive measures for admitted patients. Aim: To study the microbiological patterns and antimicrobial sensitivity of UTIs in female patients admitted to a tertiary care centre. Materials and Methods: A cross-sectional study was conducted collaboratively between the Department of Microbiology and the Department of Obstetrics and Gynaecology at RKDF Medical College Hospital and Research Centre, Bhopal, Madhya Pradesh, India. Urine samples were collected from all admitted female patients who were prescribed culture and sensitivity testing by the treating clinicians from November 2020 to October 2022. Demographic and clinical data of patients were collected, and urine samples were sent for culture-sensitivity testing. Identification and antimicrobial susceptibility testing were done using the VITEK2-compact system. Results were analysed using Statistical Packages for the Social Sciences (SPSS) version 23.0. Results: Out of 508 urine samples sent for culture-sensitivity testing, a culture positivity rate of 16.31% was observed. Diabetes was associated with 25 out of 83 patients. Among all UTI cases, 57.8% (n=48) had a urinary catheter. In catheterised patients, the predominant associated conditions were pregnancy, cardiovascular failure, followed by respiratory issues. Gram- negative isolates constituted 77.1% of the total bacterial isolates, Gram-positive isolates formed 12%, and fungal isolates comprised 10.8% of the total cultures. E. coli was the most frequently encountered species, comprising 55.4% of the isolates. The study found carbapenems to be the most effective against E. coli. In the present study, Extended Spectrum Beta-Lactamase (ESBL) production was similar in uropathogenic E. coli and K. pneumoniae, 65.9% and 64.7%, respectively. The present study study showed that aminoglycosides and nitrofurantoin are the optimal drugs for ESBL-producing organisms. Conclusion: UTIs prevalent in hospitalised women are associated with prolonged catheterisation and co-morbidities such as diabetes and cardiovascular conditions. Gram-negative bacteria are the predominant species, and their susceptibility pattern is increasingly shifting towards higher antibiotics.