Miracle-dz/UniFAR-FTUs huggingface dataset:
Flexibility in the Energy Balancing Network of Photosynthesis Enables Safe Operation under Changing Environmental Conditions

Given their ability to harness chemical energy from the sun and generate the organic compounds necessary for life, photosynthetic organisms have the unique capacity to act simultaneously as their own power and manufacturing plant. This dual capacity presents many unique challenges, chiefly that energy supply must be perfectly balanced with energy demand to prevent photodamage and allow for optimal growth. From this perspective, we discuss the energy balancing network using recent studies and a quantitative framework for calculating metabolic ATP and NAD(P)H demand using measured leaf gas exchange and assumptions of metabolic demand. We focus on exploring how the energy balancing network itself is structured to allow safe and flexible energy supply. We discuss when the energy balancing network appears to operate optimally and when it favors high capacity instead. We also present the hypothesis that the energy balancing network itself can adapt over longer time scales to a given metabolic demand and how metabolism itself may participate in this energy balancing.
Analysis of Let-7 Family miRNA in Plasma as Potential Predictive Biomarkers of Diagnosis for Papillary Thyroid Cancer

The most common histological type of thyroid cancer is papillary thyroid carcinoma (PTC). Radical resection of the thyroid gland is currently the recommended method of treatment. Almost 75% of thyroidectomies performed just for diagnostic purposes are benign. Thus, the confirmation of innovative and more precise noninvasive biomarkers holds promise for the detection of PTC, which may decrease the number of unnecessary thyroid lobectomies. In this work, using the droplet digital PCR (ddPCR) method, we have analyzed the level of five miRNAs (let-7a, let-7c, let-7d, let-7f, and let-7i) in the plasma of patients with PTC and compared them with those of a healthy control group to investigate whether miRNAs also have value in the management of PTC. Levels of four miRNAs, namely let-7a, let-7c, let-7d, and let-7f, were significantly higher in PTC patients than healthy controls. Thus, the analysis of circulating let-7 can be a useful tool and support the currently used methods for PTC diagnosis. However, our observation requires further research on a larger patient group.
Life history predicts flight muscle phenotype and function in birds.

1. Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals' ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. 2. We asked how age- and sex-dependent demands on flight muscle function are reconciled in birds. The flight muscle is an essential multifunctional organ, mediating a large range of functions associated with powered flight and thermoregulation. These functions must be balanced over an individual's lifetime. 3. We leveraged within- and between-species comparisons in a clade of small passerines (Tarsiger bush-robins) from the eastern edge of the Qinghai-Tibet Plateau. We integrated measurements of flight muscle physiology, morphology, behavior, phenology, and environmental data, analyzing trait data within a context of three widespread, adaptive life-history strategies - sexual dichromatism, age and sex-structured migration, and delayed plumage maturation. This approach provides a framework of the selective forces that shape functional variation within and between species. 4. We found more variation in flight muscle traits within species than has been previously described between species of birds under 20 g. This variation was associated with the discovery of mixed muscle fiber types (i.e. both fast glycolytic and fast oxidative fibers), which differ markedly in their physiological and functional attributes. This result is surprising given that the flight muscles of small birds are generally thought to contain only fast oxidative fibers, suggesting a novel ecological context for glycolytic muscle fibers in small birds. Within each species, flight muscle phenotypes varied by age and sex, reflecting the functional demands at different life-history stages and the pressures that individuals face as a result of their multi-class identity (i.e. species, age, and sex). 5. Our findings reveal new links between avian physiology, ecology, behavior, and life history, while demonstrating the importance of demographic-dependent selection in shaping functional phenotypic variation.
Neoadjuvant or Adjuvant Therapy for Resectable or Borderline Resectable Pancreatic Cancer: Which Is Preferred?

Pancreas ductal adenocarcinoma (PDAC) is a lethal malignancy with an increasing incidence and is characterized by nonspecific symptoms and late presentation, with a majority of patients presenting with advanced-stage disease. Incremental improvement in survival has been demonstrated in the treatment of advanced PDAC with the advent of multi-agent cytotoxic regimens, including fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX), gemcitabine and nab-paclitaxel, and nanoliposomal irinotecan and infusional flurouracil. Approximately 25%-30%of patients present with localized PDAC, either de novo resectable or primarily venous vasculature (borderline resectable), where after preoperative therapy, surgical resection is feasible and therapeutic goals are curative in intent. A traditional therapeutic paradigm is initial surgery followed by adjuvant therapy for patients with resectable disease, and recent data support that modified FOLFIRINOX (mFOLFIRINOX) provides the best oncologic outcome compared with a prior standard of single-agent gemcitabine in a highly select patient population (median overall survival [OS], 54.4 v 35 months; hazard ratio [HR], 0.48; 95% CI, 0.48 to 0.86; P 5 .003). Other adjuvant therapy options include gemcitabine and capecitabine or, speculatively, gemcitabine and nab-paclitaxel, although for the latter regimen, the adjuvant trial that evaluated the doublet compared with single-agent gemcitabine (APACT) was negative with regard to the primary end point of diseasefree survival, with a modest OS benefit observed. Outcomes with regard to the utility of adjuvant chemotherapy, and specifically adjuvant (chemo)radiation, after an R0 or R1 surgical resection and systemic therapy are pending from RTOG 0848, a randomized phase III trial, with results anticipated in 2020 (ClinicalTrials.gov identifier: NCT01013649). The past decade has seen a significant increase in the use of neoadjuvant systemic therapy, with or without the use of radiation, for both resectable and borderline resectable PDAC primarily on the basis of expert consensus, and singlearm and single-institution studies from highly select centers have reported favorable survival outcomes. A major unanswered question for early-stage resectable and borderline resectable PDAC is whether neoadjuvant therapy represents a superior therapeutic strategy over initial surgical resection and adjuvant therapy, particularly in reference to resectable PDAC.
Reprogramming the Constant Region of Immunoglobulin G Subclasses for Enhanced Therapeutic Potency against Cancer

The constant region of immunoglobulin (Ig) G antibodies is responsible for their effector immune mechanism and prolongs serum half-life, while the fragment variable (Fv) region is responsible for cellular or tissue targeting. Therefore, antibody engineering for cancer therapeutics focuses on both functional efficacy of the constant region and tissue- or cell-specificity of the Fv region. In the functional aspect of therapeutic purposes, antibody engineers in both academia and industry have capitalized on the constant region of different IgG subclasses and engineered the constant region to enhance therapeutic efficacy against cancer, leading to a number of successes for cancer patients in clinical settings. In this article, we review IgG subclasses for cancer therapeutics, including (i) IgG1, (ii) IgG2, 3, and 4, (iii) recent findings on Fc receptor functions, and (iv) future directions of reprogramming the constant region of IgG to maximize the efficacy of antibody drug molecules in cancer patients.
The evolution of the vestibular apparatus in apes and humans

Phylogenetic relationships among extinct hominoids (apes and humans) are controversial due to pervasive homoplasy and the incompleteness of the fossil record. The bony labyrinth might contribute to this debate, as it displays strong phylogenetic signal among other mammals. However, the potential of the vestibular apparatus for phylogenetic reconstruction among fossil apes remains understudied. Here we test and quantify the phylogenetic signal embedded in the vestibular morphology of extant anthropoids (monkeys, apes and humans) and two extinct apes (Oreopithecus and Australopithecus) as captured by a deformation-based 3D geometric morphometric analysis. We also reconstruct the ancestral morphology of various hominoid clades based on phylogenetically-informed maximum likelihood methods. Besides revealing strong phylogenetic signal in the vestibule and enabling the proposal of potential synapomorphies for various hominoid clades, our results confirm the relevance of vestibular morphology for addressing the controversial phylogenetic relationships of fossil apes.
pH-Dependent Foam Formation Using Amphoteric Colloidal Polymer Particles

Near-monodispersed micrometer-sized polystyrene (PS) particles carrying amidino and carboxyl groups on their surfaces were synthesized by soap-free emulsion polymerization using an amphoteric free radical initiator. The resulting amphoteric PS particles were characterized in terms of diameter, morphology, disperibility in aqueous media and surface charge using scanning electron microscopy (SEM), optical microscopy (OM), sedimentation rate and electrophoretic measurements. At pH 2.0, where the amidino groups are protonated (positively charged), and at pH 11.0, where the carboxyl groups are deprotonated (negatively charged), the PS particles were well dispersed in aqueous media via electrostatic repulsion. At pH 4.8, where the surface charges are neutral, the PS particles were weakly aggregated. Furthermore, it was confirmed that the PS particles can function as a pH-sensitive foam stabilizer: foamability and foam stability were higher at pH 2.0 and 4.8, where the PS particles can be adsorbed to the air–water interface, and lower at pH 11.0, where the PS particles tend to disperse in bulk aqueous medium. SEM and OM studies indicated that hexagonally close-packed arrays of PS particles were formed on the bubble surfaces and moiré patterns were observed on the dried foams. Moreover, the fragments of dried foams showed iridescent character under white light.
Perioperative Hyperoxyphobia: Justified or Not? Benefits and Harms of Hyperoxia during Surgery

The use of an inspiratory oxygen fraction of 0.80 during surgery is a topic of ongoing debate. Opponents claim that increased oxidative stress, atelectasis, and impaired oxygen delivery due to hyperoxic vasoconstriction are detrimental. Proponents point to the beneficial effects on the incidence of surgical site infections and postoperative nausea and vomiting. Also, hyperoxygenation is thought to extend the safety margin in case of acute intraoperative emergencies. This review provides a comprehensive risk-benefit analysis for the use of perioperative hyperoxia in noncritically ill adults based on clinical evidence and supported by physiological deduction where needed. Data from the field of hyperbaric medicine, as a model of extreme hyperoxygenation, are extrapolated to the perioperative setting. We ultimately conclude that current evidence is in favour of hyperoxia in noncritically ill intubated adult surgical patients.
Integration of Mixed Methods in Community-Based Participatory Research: Development of a Disease Prevention Intervention for Ultra-Orthodox Jewish Women

Purpose: To describe the development of the first disease prevention intervention with ultra-Orthodox Jewish (UOJ) women in Israel using mixed methods and community-based participatory research (CBPR). Design: This collaborative, 7-staged development process used an exploratory sequential mixed methods design integrated into a community-based participatory approach. Setting: The UOJ community in Israel, a high-risk, low socioeconomic, culturally insular minority that practices strict adherence to religious standards, maintains determined seclusion from mainstream culture and preserves traditional practices including extreme modesty and separation between the sexes. Participants: Women from a targeted UOJ community in Israel with distinct geographic, religious, and cultural parameters. These included 5 key informant interviewees, 5 focus groups with 6 to 8 participants in each, a cluster randomized sample of 239 questionnaire respondents (an 87% response rate), and 11 steering committee participants. Method: Qualitative data were analyzed through Interpretative Phenomenological Analysis by 2 researchers. Quantitative data were collected via questionnaire (designed based on qualitative findings) and analyzed utilizing descriptive statistics. Results: Barriers to health behavior engagement and intervention preferences were identified. The final intervention included walking programs, health newsletters, community leader trainings, teacher and student trainings, and health integration into schools. Conclusion: Utilizing mixed methods in CBPR improved cultural tailoring, potentially serving as a model for intervention design in other difficult to access, low socioeconomic, and culturally insular populations.
Deciphering the Virome of Culex vishnui Subgroup Mosquitoes, the Major Vectors of Japanese Encephalitis, in Japan

Japanese encephalitis (JE) remains a public health concern in several countries, and the Culex mosquito plays a central role in its transmission cycle. Culex mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses) that cause human and animal diseases. The current trend of studies displays enhanced efforts to characterize the mosquito virome through bulk RNA sequencing due to possible arbovirus–ISV interactions; however, the extent of viral diversity in the mosquito taxon is still poorly understood, particularly in some disease vectors. In this study, arboviral screening and RNA virome analysis of Culex tritaeniorhynchus and C. pseudovishnui, which are part of the Culex vishnui subgroup mosquitoes, were performed. Results from these two mosquito species, known as the major vectors of JE virus (JEV) in Asia, collected in three prefectures in Japan were also compared with the sympatric species C. inatomii. A total of 27 viruses, including JEV, were detected from these Culex mosquitoes. Molecular and phylogenetic analyses of the detected viruses classified 15 of the 27 viruses as novel species, notably belonging to the Flaviviridae, Rhabdoviridae, Totiviridae, and Iflaviridae families. The successful isolation of JEV genotype I confirmed its continuous presence in Japan, suggesting the need for periodic surveillance. Aside from JEV, this study has also reported the diversity of the RNA virome of disease vectors and broadened the knowledge on mosquito virome profiles containing both arbovirus and ISV. Mosquito taxon seemed to contribute largely to the virome structure (e.g., virome composition, diversity, and abundance) as opposed to the geographical location of the mosquito species. This study therefore offers notable insights into the ecology and evolution of each identified virus and viral family. To the authors’ knowledge, this is the first study to characterize the viromes of the major JE vectors in Japan.
New Antimicrobial Phenyl Alkenoic Acids Isolated from an Oil Palm Rhizosphere-Associated Actinomycete, Streptomyces palmae CMU-AB204T

Basal stem rot (BSR), or Ganoderma rot disease, is the most serious disease associated with the oil palm plant of Southeast Asian countries. A basidiomycetous fungus, Ganoderma boninense, is the causative microbe of this disease. To control BSR in oil palm plantations, biological control agents are gaining attention as a major alternative to chemical fungicides. In the course of searching for effective actinomycetes as potential biological control agents for BSR, Streptomyces palmae CMU-AB204T was isolated from oil palm rhizosphere soil collected on the campus of Chiang Mai University. The culture broth of this strain showed significant antimicrobial activities against several bacteria and phytopathogenic fungi including G. boninense. Antifungal and antibacterial compounds were isolated by antimicrobial activity-guided purification using chromatographic methods. Their structures were elucidated by spectroscopic techniques, including Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), Ultraviolet (UV), and Infrared (IR) analyses. The current study isolated new phenyl alkenoic acids 1–6 and three known compounds, anguinomycin A (7), leptomycin A (8), and actinopyrone A (9) as antimicrobial agents. Compounds 1 and 2 displayed broad antifungal activity, though they did not show antibacterial activity. Compounds 3 and 4 revealed a strong antibacterial activity against both Gram-positive and Gram-negative bacteria including the phytopathogenic strain Xanthomonas campestris pv. oryzae. Compounds 7–9 displayed antifungal activity against Ganoderma. Thus, the antifungal compounds obtained in this study may play a role in protecting oil palm plants from Ganoderma infection with the strain S. palmae CMU-AB204T.
Cyclooxygenases Inhibitors Efficiently Induce Cardiomyogenesis in Human Pluripotent Stem Cells

Application of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) is limited by the challenges in their efficient differentiation. Recently, the Wingless (Wnt) signaling pathway has emerged as the key regulator of cardiomyogenesis. In this study, we evaluated the effects of cyclooxygenase inhibitors on cardiac differentiation of hPSCs. Cardiac differentiation was performed by adherent monolayer based method using 4 hPSC lines (HES3, H9, IMR90, and ES4SKIN). The efficiency of cardiac differentiation was evaluated by flow cytometry and RT-qPCR. Generated hPSC-CMs were characterised using immunocytochemistry, electrophysiology, electron microscopy, and calcium transient measurements. Our data show that the COX inhibitors Sulindac and Diclofenac in combination with CHIR99021 (GSK-3 inhibitor) efficiently induce cardiac differentiation of hPSCs. In addition, inhibition of COX using siRNAs targeted towards COX-1 and/or COX-2 showed that inhibition of COX-2 alone or COX-1 and COX-2 in combination induce cardiomyogenesis in hPSCs within 12 days. Using IMR90-Wnt reporter line, we showed that inhibition of COX-2 led to downregulation of Wnt signalling activity in hPSCs. In conclusion, this study demonstrates that COX inhibition efficiently induced cardiogenesis via modulation of COX and Wnt pathway and the generated cardiomyocytes express cardiac-specific structural markers as well as exhibit typical calcium transients and action potentials. These cardiomyocytes also responded to cardiotoxicants and can be relevant as an in vitro cardiotoxicity screening model.
An observational study of ECCO Finishing’s selling channels

This paper focuses on a strategic decision of a Swedish company. The company is ECCO Finishing and it sells its products in many countries. It assembles and installs painting guns and sells them through two main channels: one is via its own subsidiaries based on the targeted countries and the other is via distributors. And for the distributors, some sell exclusively ECCO products and some sell many other products as well. All of these channels have advantages and disadvantages and which one should be used in a particular country is of great interest to the management. In this paper an advanced causal inference method named propensity score on three/two level treatments is applied for discussing this question. Based on the results of the Generalized Linear Mixed models as well as a simple linear model, conclusions have been drawn about which country should be treated in which channel.
EXPLICIT SOLUTIONS FOR CONTINUOUS-TIME QBD PROCESSES BY USING RELATIONS BETWEEN MATRIX GEOMETRIC ANALYSIS AND THE PROBABILITY GENERATING FUNCTIONS METHOD

Two main methods are used to solve continuous-time quasi birth-and-death processes: matrix geometric (MG) and probability generating functions (PGFs). MG requires a numerical solution (via successive substitutions) of a matrix quadratic equation A0 + RA1 + R2A2 = 0. PGFs involve a row vector $\vec{G}(z)$ of unknown generating functions satisfying $H(z)\vec{G}{(z)^\textrm{T}} = \vec{b}{(z)^\textrm{T}},$ where the row vector $\vec{b}(z)$ contains unknown “boundary” probabilities calculated as functions of roots of the matrix H(z). We show that: (a) H(z) and $\vec{b}(z)$ can be explicitly expressed in terms of the triple A0, A1, and A2; (b) when each matrix of the triple is lower (or upper) triangular, then (i) R can be explicitly expressed in terms of roots of $\det [H(z)]$; and (ii) the stability condition is readily extracted.
INTRUSION DETECTION BY MACHINE LEARNING

s in conference proceedings Brunner, C. (2019): Behatolás-detektálás Tensorflow Platformon. 16. Országos Gazdaságinformatikai Konferencia (p. 32). Budapest: NJSZT Neumann János Számítógép-tudományi Társaság GIKOF Gazdaságinformatikai Kutatási és Oktatási Fórum. Brunner, C. (2018): Hálózati behatolás detektálás Neurális hálózatok összevonásával. OGIK’2018 Országos Gazdaságinformatikai Konferencia – Az előadások összefoglalói (p. 75). Sopron, Alexander Alapítvány a Jövő Értelmiségéért. Brunner, C. (2017): Ant Colony Algorithm in Data Mining. XIV. Országos GazdaságInformatikai Konferencia (p. 31). Győr: Alexander Alapítvány a Jövő Értelmiségéért. Brunner, C. (2016): Behatolási adatok feldolgozása gépi tanulás és MapReduce segítségével. XIII. Országos Gazdaságinformatikai Konferencia (pp. 25-26). Dunaújváros: DUE Press. Conference presentations Brunner C. (2019): Behatolás-detektálás Tensorflow PlatformonPresented at: 16. Országos Gazdaságinformatikai Konferencia; Nov 8-9; Budapest, Hungary Brunner, C. (2018): Hálózati behatolás detektálás Neurális hálózatok összevonásával. Presented at: OGIK’2018 Országos Gazdaságinformatikai Konferencia; Nov 9-10; Sopron, Hungary Brunner, C. (2017): Ant Colony Algorithm in Data Mining. Poster presented at: XIV. Országos GazdaságInformatikai Konferencia; Nov 10-11; Sopron, Hungary. Brunner, C. (2016): Behatolási adatok feldolgozása gépi tanulás és MapReduce segítségével. Presented at: XIII. Országos GazdaságInformatikai Konferncia; Nov 11-12; Dunaújváros, Hungary.