Miracle-dz/UniFAR-FTUs huggingface dataset:
Cortical encoding of melodic expectations in human temporal cortex

Humans engagement in music rests on underlying elements such as the listeners’ cultural background and general interest in music, all shaping the way music is processed in the brain and perceived. Crucially, these factors modulate how listeners anticipate musical events, a process inducing instantaneous neural responses as the music confronts these expectations. Measuring such neural correlates would represent a direct window into high-level brain processing of music. Here we recorded electroencephalographic and electrocorticographic brain responses as participants listened to Bach melodies. We assessed the relative contributions of the acoustic versus melodic components of the music to the neural signal. Acoustic features included envelope and its derivative. Melodic features included information on melodic progressions (pitch) and their tempo (onsets), which were extracted from a Markov model predicting the next note based on a corpus of Western music and the preceding proximal musical context. We related the music to brain activity with a linear temporal response function, and demonstrated that cortical responses to music encode melodic expectations. Specifically, individual-subject neural signals were better predicted by a combination of acoustic and melodic expectation features than by either alone. This effect was most pronounced at response latencies up to 350ms, and in both planum temporale and Heschl’s gyrus. Finally, expectations of pitch and onset-time of musical notes exerted independent cortical effects, and such influences were modulated by the listeners’ musical expertise. Overall, this study demonstrates how the interplay of experimental and theoretical approaches can yield novel insights into the cortical encoding of melodic expectations.
Modelling of pH-dependence to develop a strategy for stabilising mAbs at acidic steps in production

Engineered proteins are increasingly being required to function or pass through environmental stresses for which the underlying protein has not evolved. A major example in health are antibody therapeutics, where a low pH step is used for purification and viral clearance. In order to develop a computational model for analysis of pH-stability, predictions are compared with experimental data for the relative pH-sensitivities of antibody domains. The model is then applied to proteases that have evolved to be functional in an acid environment, showing a clear signature for low pH-dependence of stability in the neutral to acidic pH region, largely through reduction of saltbridges. Interestingly, an extensively acidic protein surface can maintain contribution to structural stabilisation at acidic pH through replacement of basic sidechains with polar, hydrogen-bonding groups. These observations form a design principle for engineering acid-stable proteins.
Mass Production of Highly Active NK Cells for Cancer Immunotherapy in a GMP Conform Perfusion Bioreactor

NK cells have emerged as promising candidates for cancer immunotherapy, especially due to their ability to fight circulating tumor cells thereby preventing metastases formation. Hence several studies have been performed to generate and expand highly cytotoxic NK cells ex vivo, e.g., by using specific cytokines to upregulate both their proliferation and surface expression of distinct activating receptors. Apart from an enhanced activity, application of NK cells as immunotherapeutic agent further requires sufficient cell numbers and a high purity. All these parameters depend on a variety of different factors including the starting material, additives like cytokines as well as the culture system. Here we analyzed PBMC-derived NK cells of five anonymized healthy donors expanded under specific conditions in an innovative perfusion bioreactor system with respect to their phenotype, IFNγ production, and cytotoxicity in vitro. Important features of the meander type bioreactors used here are a directed laminar flow of medium and control of relevant process parameters. Cells are cultivated under “steady state” conditions in perfusion mode. Our data demonstrate that expansion of CD3+ T cell depleted PBMCs in our standardized system generates massive amounts of highly pure (>85%) and potent anti-cancer active NK cells. These cells express a variety of important receptors driving NK cell recruitment, adhesion as well as activation. More specifically, they express the chemokine receptors CXCR3, CXCR4, and CCR7, the adhesion molecules L-selectin, LFA-1, and VLA-4, the activating receptors NKp30, NKp44, NKp46, NKG2D, DNAM1, and CD16 as well as the death ligands TRAIL and Fas-L. Moreover, the generated NK cells show a strong IFNγ expression upon cultivation with K562 tumor cells and demonstrate a high cytotoxicity toward leukemic as well as solid tumor cell lines in vitro. Altogether, these characteristics promise a high clinical potency of thus produced NK cells awaiting further evaluation.
Content of selected inorganic compounds in the eggs of hens kept in two different systems: organic and battery cage

Abstract Recent years have seen increased interest in the influence of bioactive dietary components on human genes and gene expression. A good source of many bioactive substances is the chicken egg. The egg is considered to be an excellent food provided by nature. It is a good source of nutrients such as vitamins A, B2, B6, B12, D, E and K, as well as elements including phosphorus, selenium, iron, zinc, magnesium and calcium. The research material use in this study consisted of eggs from hens kept in two different systems: organic and battery cages. The content of calcium (Ca), magnesium (Mg) and zinc (Zn) was determined in the egg contents – in the yolk and white respectively. The content of elements was determined by atomic absorption spectrometry (AAS) using an AA280 FS spectrometer with the automatic dilution of standards and samples. The eggs from the organically raised hens had a higher calcium, magnesium and zinc content. The greater variation in the Ca, Mg and Zn content in the organic eggs is due to the more individualized feeding system. The rearing system of the hens significantly affects the concentration of elements in the egg. The results of this research indicate that eggs from organic farming systems have a richer chemical composition in terms of the content of nutrients such as calcium, magnesium and zinc compared with eggs obtained from caged hens. Therefore, consumers purchasing eggs should consider the system in which the hens were reared, as eggs can be a valuable source of these elements in the diet.
Las zoonosis reemergentes bajo el enfoque de “Una salud”

La Organización Mundial de la Salud (OMS) definió en 2004 las zoonosis emergentes como aquellas recientemente descubiertas o descritas previamente pero que han evidenciado un incremento de su incidencia, expansión geográfica o variedad de huéspedes o vectores (1). El 60% de las enfermedades infecciosas que afectan al ser humano son de origen zoonótico (2) y casi un 20% de todas ellas son transmitidas por vectores. Esto refuerza la conexión entre la salud animal, humana y ambiental y la importancia del estudio de estas enfermedades en su ámbito biológico, ecológico, médico y económico para promover y garantizar la salud global.
Typha domingensis Pers. (Typhaceae): do artesanto à fitorremediação de ambientes aquáticos continentais e eutrofizados

A eutrofização de um ecossistema pode ocorrer de duas formas: artificial e natural. A eutrofização artificial está associada ao aporte de excesso de nutrientes associado às atividades antrópicas. A eutrofização natural é um processo que ocorre ao longo do envelhecimento dos ecossistemas aquáticos e consiste no aumento das concentrações de nutrientes, especialmente nitrogênio e fósforo e, consequentemente, da produtividade primária1. É considerada como uma reação em cadeia de causas e efeitos bem evidentes, cuja característica principal é a quebra relativa de estabilidade do ecossistema (homeostasia) que, fora do estado de equilíbrio, passa a produzir mais matéria orgânica do que é capaz de consumir2. Esse impacto pode provocar diversos danos, entre eles: desenvolvimento intenso e descontrolado do fitoplâncton devido à alta disponibilidade de nutrientes; degradação da qualidade da água com alterações de composição, cor, turbidez e transparência; aumento da decomposição, o que causa um maior consumo de oxigênio dissolvido (podendo levar à anoxia do ecossistema) e produção de gases que causam maus odores; produção de substâncias tóxicas; prejuízos consideráveis para o uso da água em abastecimento, irrigação, aproveitamentos hidrelétricos, recreação, turismo e paisagismo, entre outros3. As plantas aquáticas também passam a apresentar intenso desenvolvimento devido à alta disponibilidade de nutrientes na água, o que pode, além de levar à competição entre espécies vegetais, alterar a qualidade da água, uma vez que reduz a entrada de luz no ecossistema.
HdaB: a novel and conserved DnaA-related protein that targets the RIDA process to stimulate replication initiation

Exquisite control of the DnaA initiator is critical to ensure that bacteria initiate chromosome replication in a cell cycle-coordinated manner. In many bacteria, the DnaA-related and replisome-associated Hda/HdaA protein interacts with DnaA to trigger the regulatory inactivation of DnaA (RIDA) and prevent over-initiation events. In the C. crescentus Alphaproteobacterium, the RIDA process also targets DnaA for its rapid proteolysis by Lon. The impact of the RIDA process on adaptation of bacteria to changing environments remains unexplored. Here, we identify a novel and conserved DnaA-related protein, named HdaB, and show that homologs from three different Alphaproteobacteria can inhibit the RIDA process, leading to over-initiation and cell death when expressed in actively growing C. crescentus cells. We further show that HdaB interacts with HdaA in vivo, most likely titrating HdaA away from DnaA. Strikingly, we find that HdaB accumulates mainly during stationary phase and that it shortens the lag phase upon exit from stationary phase. Altogether, these findings suggest that expression of hdaB during stationary phase prepares cells to restart the replication of their chromosome as soon as conditions improve, a situation often met by free-living or facultative intracellular Alphaproteobacteria.
Brazil’s new president and ‘ruralists’ threaten Amazonia’s environment, traditional peoples and the global climate

Summary Jair Bolsonaro (Brazil’s new president) and “ruralists” (large landholders and their representatives) have initiated a series of measures that threaten Amazonia’s environment and traditional peoples, as well as global climate. These include weakening the country’s environmental agencies and forest code, granting amnesty to deforestation, approving harmful agrochemicals, reducing protected areas, and denying the existence of anthropogenic climate change. Both the measures themselves and the expectation of impunity they encourage have spurred increased deforestation, which contributes to climate change and to land conflicts with traditional peoples. Countries and companies that import Brazilian beef, soy and minerals are stimulating these impacts.
Functional plasticity and reversible growth behavior of patients’ acute myeloid leukemia stem cells growing in mice

Resistance against chemotherapy remains a major obstacle in treating patients with acute myeloid leukemia (AML). Novel therapeutic concepts are especially desired to target and eliminate resistant AML stem cells. Here we show that AML stem cells harbor the plasticity to switch from a low-cycling, chemotherapy resistant state into an actively proliferating state associated with treatment response. We used patient-derived xenograft (PDX) cells from patients with high risk or relapsed AML, which were lentivirally transduced for marker expression, stained with the proliferation-sensitive dye Carboxyfluorescein succinimidyl ester (CFSE), and re-transplanted into next-recipient mice. A rare subpopulation of AML cells displayed reduced proliferation in vivo, associated with increased treatment resistance. The proportion of AML cells with stem cell potential was identical in both, the highly and lowly proliferative sub-fraction. In re-transplantation experiments, proliferation behavior proved reversible, and AML stem cells were able to switch between a high and low proliferation state. Our data indicate that AML stem cells display functional plasticity in vivo, which might be exploited for therapeutic purposes, to prevent AML relapse and ultimately improve the prognosis of patients with AML.
An Experimental Approach to Exploring Market Responses in Small-Scale Fishing Communities

Small-scale fishing communities are increasingly connected to international seafood trade via exports to a growing global market. Understanding how this connectedness impacts local fishery systems, both socially and ecologically, has become a necessary challenge for fisheries governance. Market prices are a potential mechanism by which global market demands are transferred to small-scale fishery actors. In most small-scale fisheries this happens through various traders (intermediaries, middlemen/women or patrons). By financing fishing operations, buying and selling products and transferring market information, traders can actively pass international market signals, such as price, to fishers. How these signals influence fishers' decisions and consequent fishing effort is still poorly understood yet significant for future social-ecological sustainability. The paper uses an economic framed field experiment, in combination with interviews, to shed light on this. It does so in the context of the Philippine patron-client 'suki' arrangement. Over 250 fishers in Concepcion, Iloilo were asked in an economic experiment, to make decisions about fuel loans in light of changing market prices. Interviews with participants and their patrons gathered additional information on relevant contextual variables potentially influencing borrowing. They included fisher characteristics and socio-economic conditions. Contrary to our hypotheses, fishers showed no response in their borrowing behaviour to experimental price changes. Instead, gender and the previous experiment round were predictive of their choice of loans in the experiment. We explore possible reasons for this.
Is REDD+ More of an Institutional Affair than a Market Process? The Concealed Social and Cultural Consequences of an Ongoing REDD+ Project in Kolo Hills, Tanzania

The neo-liberal rationale behind REDD programs aims to create a market for common resources, with monetary payment incentives as the most important driver for conservation initiatives. In reality, however, the chain of implementation from UN to village, encompassing numerous processes of design, planning, and practices at distinct levels and contexts, is more institutional and political than economic. This research project follows the planning and implementation process of a REDD+ project in the Kolo Hills, Tanzania. The analysis showed that the project’s main objectives were poorly understood by the men and women of the target group, who interpreted it as yet another top-down postcolonial project. The target group’s interpretations also made them act in accordance with their own cultural rationality and logic of practice and not as the donors and project implementers had assumed. The project objectives of the payment system, consciousness awareness and engagement of the target population, thus, seem to have failed, despite the donors’ and implementers’ claim of success.
Comparison of Two Rift Valley Fever Serological Tests in Cameroonian Cattle Populations Using a Bayesian Latent Class Approach

Rift Valley Fever is an important zoonotic viral disease of livestock occurring across much of Africa causing acute febrile illness, abortion, and neonatal death in livestock particularly sheep and cattle and a range of disease in humans from mild flu-like symptoms to more severe haemorrhagic fever and death. Understanding the epidemiology requires well-evaluated tools including antibody detection ELISAs. It is well-recognized that tests developed in one population do not necessarily perform as well when used in different populations and it is therefore important to assess tests in the populations in which they are to be used. Here we describe the performance of a commercial RVF ELISA (ID.Vet) and an in-house plaque reduction neutralization test (PRNT80). A Bayesian no gold standard latent class model for two tests and ≥2 populations based on the Hui-Walter model was used to estimate the test parameters using a range of populations based on geographical separation and age to assess consistency of performance across different sub-populations. The ID.Vet ELISA had an estimated diagnostic sensitivity (Se) of 0.854 (0.655–0.991 95%BCI) and specificity (Sp) of 0.986 (0.971–0.998 95%BCI) using all the data and splitting the population by geographical region compared to 0.844 (0.660–0.973 95%BCI) and 0.981 (0.965–0.996 95%BCI) for the PRNT80. There was slight variation in the mean Se and Sp in different sub-populations mainly in Se estimates due to small numbers of positives in the sub-populations but the 95% BCI generally overlapped suggesting a very consistent performance across the different geographical areas and ages of animals. This is one of few reports of serological evidence of RVF in Central Africa and strongly suggests the virus is actively circulating in this cattle population. This has important public health implications and RVF should be considered as a differential in both livestock disease cases as well as human febrile cases in West and Central Africa not just East Africa. We also demonstrate that the performance of the commercial ELISA is comparable to the PRNT80 but has the advantages of speed, lower cost and no containment needs making it a much more useful test for low and middle income settings (LMICs).
kASA: Taxonomic Analysis of Metagenomic Data on a Notebook

The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available software tools for that purpose either consume large amounts of RAM or yield an insufficient quality of the results. Here we present kASA, a k-mer based software capable of identifying and profiling metagenomic sequences with high computational efficiency and a small user-definable memory footprint. We ensure high sensitivity and precision via k-mers on amino acid level with a dynamic length of multiple k’s. Custom algorithms and data structures that are optimised for external memory storage enable for the first time a full-scale metagenomics analysis without compromise on a standard notebook.
Regulatory T cells shape the CD4 T cell response to Salmonella

FoxP3+ regulatory T cells (Tregs) play an important role in controlling inflammation and maintaining homeostasis at mucosal sites. Tregs may also limit immunopathology during infection but their role in this context remains poorly understood. CD4 T helper (Th) cells are important drivers of immune responses and can express master transcription factors (TFs) including T-bet, GATA3 and RORγT, which identify Th1, Th2 and Th17 cells, respectively. Tregs can also express these TFs, and recent research suggests that Tregs expressing master TFs may be able to selectively suppress their corresponding Th subsets. T-bet+ Tregs have been shown to selectively target Th1 cells in some contexts, but it is unclear whether the same dynamic occurs with Tregs expressing other TFs. It is also unclear whether selective suppression can influence the overall CD4 T cell bias during infection. To address these questions, an infection model using Salmonella enterica serotype Typhimurium (STM) was developed to induce non-lethal colitis. This allowed STM-specific and polyclonal CD4 T cells to be tracked in multiple tissues. Using this model, a dynamic and site-specific CD4 T cell response was revealed. An early and transient colonic Th17 response was followed by a sustained Th1 bias. This Th response develops in parallel with an early increase in the proportion of T-bet+ Tregs and a later increase in the proportion of RORγT+ Tregs. This reciprocal dynamic between Th subsets and Tregs expressing the same TF is consistent with the hypothesis that specific populations of Tregs selectively suppress Th subsets. To determine if Tregs are required for the dynamic Th bias, Treg depletion experiments were carried out at different timepoints. Results show that Tregs are essential for both the early Th17 response and the later Th1 response. Together, these results support the hypothesis that Tregs shape the dynamic Th bias by selective suppression. Further research is needed to address what mechanism might drive this targeted regulation. This research shows the potential for Tregs to not just inhibit the overall T cell response, but to actively shape Th bias. This highlights the potential for Tregs expressing specific TFs to be used in targeted therapeutic approaches. Further work is warranted to improve our basic understanding of how Tregs shape immunity and to develop appropriate clinical applications.
Standard Cultivar Selection and Digital Quantification for Precise Classification of Maturity Groups in Soybean

The maturity group (MG) system is widely used to group soybean [Glycine max (L.) Merr. ] varieties based on their growth periods and photothermal responses. However, there is still no universal standard or quantifiable methodology for MG classification. In this study, phenological traits of 107 Chinese, 4 Far East Russian representative soybean varieties, and 113 North American reference varieties covering 13 MGs were evaluated at eight locations (ranging from 30 to 50° N) in four ecoregions of China for two consecutive years (2014 and 2015). Relative maturity groups (RMGs) were attributed to all the varieties based on the linear regression models. To decimalize the RMG values of the early-maturing varieties belonging to MGs below 0, negative values were defined for MGs 00, 000, and 0000. The additive main effects and multiplicative interaction (AMMI) model was used to screen 185 standard candidate varieties for MGs 0000 to VIII. This study provided a systematic and quantifiable methodology for RMG identification in soybeans. The methodology is expected to be widely adopted by soybean regionalization and germplasm exchanges throughout the world and will be helpful for characterizing the photothermal sensitivity and adaptability of the given soybean varieties.