Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of vegetation dynamics in the control of atmospheric CO2 content

This thesis contains a description of the Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ-DGVM) and its application to infer the role of vegetation dynamics on atmospheric CO2 content at different time-scales. The model combines vegetation dynamics and biogeochemistry in a modular framework. Individual modules describe ecosystems processes, including vegetation resource competition and production, tissue turnover, growth, fire and mortality, soil and litter biogeochemistry, including the effects of CO2 on these processes. The model simulates realistic post-disturbance succession in different environments. Seasonal exchange of H2O and CO2 between the terrestrial biosphere and the atmosphere is modelled in reasonable agreement with observation. Global estimates of carbon stocks in soil, litter and vegetation are within their acceptable ranges and the model captures the present-day patterns in vegetation. Fire return intervals are simulated correctly in most regions. Results emphasise the important role of the terrestrial biosphere in both the seasonal cycle and in the inter-annual variability in the growth rate of atmospheric CO2. LPJ successfully reproduced both the amplitude and phase of the seasonal cycle of atmospheric CO2 content as measured at a global network of monitoring stations. The model predicted a small net terrestrial biosphere uptake of CO2 during the 1980's with a strong CO2 fertilisation effect, which enhances plant production, reduced by the effects of climate and land use change. Historical land use change and CO2 fertilisation have been the dominant, albeit opposing factors governing the response of the terrestrial biosphere with respect to carbon storage during the 20th century. LPJ is run using one future climate and atmospheric CO2 scenario until 2200. Enhanced production due to the CO2 fertilisation effect eventually reaches an asymptote, and consequently the ability of the terrestrial biosphere to store additional carbon diminishes. At the end of the forcing period, vegetation is no longer in equilibrium, justifying the need for dynamic models in global change research. LPJ predicts the abundance of woody vegetation to increase everywhere, except in regions facing large reductions in precipitation. The tree-line extends northwards and temperate woody plants expand into the present-day boreal forest. (Less)
Unmodified Half-Gates is Adaptively Secure - So is Unmodified Three-Halves

Adaptive security is a crucial property for garbling schemes in pushing the communication of garbled circuits to an offline phase when the input is unknown. In this paper, we show that the popular half-gates scheme by Zahur et al. (Eurocrypt’15), without any modification, is adaptively secure in the non-programmable random permutation model (npRPM). Since real implementations of selective-secure half-gates are already based on npRPM, our result shows that these implementations are already adaptively secure under the same condition where the selective security is proven. Additionally, we expand our analysis to cover the recent three-halves construction by Rosulek and Roy (Crypto’21); we also discuss some optimizations and separation when considering the programmable random permutation model instead.
Socio-Cultural Factors and Experiences of School Going Teenage Mothers in Rural Zambia: A Phenomenological Study.

Background: Teenage pregnancies disproportionately affect developing countries more than developed countries. This study aimed to explore the social-cultural dynamics and experiences of teenage school-going mothers in a rural district of the Eastern Province of Zambia to understand the lived experiences of teenage mothers in-depth. Methods: This was a phenomenological study done in two schools in one of the provinces with the highest teenage pregnancy rates in Zambia. Data were analysed thematically in a deductive approach using a framework from a recent systematic review done in studies on teenage pregnancies from sub-Saharan Africa. A total of 26 school-going adolescents and young mothers were interviewed. Results: The majority came from poor households in rural areas and lacked knowledge and access to sex education and contraceptive services before falling pregnant. Cultural beliefs and traditional practices fuel misconceptions about contraceptives and condom use and create a narrative/expectation among the girls of wanting to experience sex. They experienced rejection and stigma during pregnancy and were now experiencing hardships in fending for themselves and their babies. Contemporary programs were either non-existent or did not adequately address the economic and psychosocial challenges being faced by teenage mothers, highlighting the need for more responsive interventions. Conclusion: This study found that teenage and young mothers who re-entered school were more likely to be from poor and large families, first-borns and in day schools. Traditional beliefs and cultural practices influence. They experience discrimination, rejection, low self-esteem and economic hardships.
Environmental DNA transformation resulted in an active phage in Escherichia coli

The achievement of an active biological entity from environmental DNA is important in the field of phage. In this study, the environmental DNA extracted from hospital wastewater was transferred into Escherichia coli DH10B and Escherichia coli BL21 with chemical transformation and electroporation. After transformation, overnight cultures were filtered and used as phage source. The efficacies of the techniques were evaluated with spot test and double-layer agar assay. The emerged phage, named as ADUt, was purified and host-range analysis was performed. Phage DNA was isolated, sequenced and restriction profile was determined. The genome was assembled. The phylogenetic tree was constructed via VipTree. The extracted DNA resulted in active phage by the transformation of E. coli DH10B, but not E. coli BL21. The chemical transformation was found more successful than electroporation. ADUt phage was found to be polyvalent and effective against limited strains of Shigella and Escherichia genera. The phage genome size and GC ratio are 166904 bp and 35.67%, respectively. ADUt is a member of Straboviridae family and Tequatrovirus genus. This is the first study that uses environmental DNA for acquiring active phage, which may be an important source of new phage discovery. The result showed that DNA transformation yields active bacteriophage with both chemical transformation and electroporation.
Photovoltaic properties of new solar cell based on ideal cubic NaNbO3 thin films: a combined experimental and density functional theory study

We explore the photovoltaic properties of a novel homojunction solar cell based on NNO(p)/NNO(n) perovskite by employing a combination of material synthesis, characterization and density functional theory calculations that are novel ideas compared to those previously reported in the literature. The band structure reveals that NaNbO3 introduces a n-type semiconductor. Moreover, using DFT calculation, we created n-NNO by a simple substitution in the O site by 4.16% fluorine atoms. Experimental and DFT calculation reveals that NNO perovskite exhibits a direct bandgap of ∼1.6 eV, with a slightly larger two other direct bandgaps of ∼2.13 and 3.24 eV. After extracting the necessary parameters, an electrical modelization of an n-NNO/p-NNO solar cell is performed by Maple software revealed that the cell conversion efficiency can reach 17% which presents a first path to identify a new solar cell based only on perovskite material.
Striatal Dopamine Signals and Reward Learning

Abstract We are constantly bombarded by sensory information and constantly making decisions on how to act. In order to optimally adapt behavior, we must judge which sequences of sensory inputs and actions lead to successful outcomes in specific circumstances. Neuronal circuits of the basal ganglia have been strongly implicated in action selection, as well as the learning and execution of goal-directed behaviors, with accumulating evidence supporting the hypothesis that midbrain dopamine neurons might encode a reward signal useful for learning. Here, we review evidence suggesting that midbrain dopaminergic neurons signal reward prediction error, driving synaptic plasticity in the striatum underlying learning. We focus on phasic increases in action potential firing of midbrain dopamine neurons in response to unexpected rewards. These dopamine neurons prominently innervate the dorsal and ventral striatum. In the striatum, the released dopamine binds to dopamine receptors, where it regulates the plasticity of glutamatergic synapses. The increase of striatal dopamine accompanying an unexpected reward activates dopamine type 1 receptors (D1Rs) initiating a signaling cascade that promotes long-term potentiation of recently active glutamatergic input onto striatonigral neurons. Sensorimotor-evoked glutamatergic input, which is active immediately before reward delivery will thus be strengthened onto neurons in the striatum expressing D1Rs. In turn, these neurons cause disinhibition of brainstem motor centers and disinhibition of the motor thalamus, thus promoting motor output to reinforce rewarded stimulus-action outcomes. Although many details of the hypothesis need further investigation, altogether, it seems likely that dopamine signals in the striatum might underlie important aspects of goal-directed reward-based learning.
Mechanistic insights into the role of probiotics in modulating immune cells in ulcerative colitis

Ulcerative colitis (UC) is a persistent inflammatory disorder that affects the gastrointestinal tract, mainly the colon, which is defined by inflammatory responses and the formation of ulcers. Probiotics have been shown to directly impact various immune cells, including dendritic cells (DCs), macrophages, natural killer (NK) cells, and T and B cells. By interacting with cell surface receptors, they regulate immune cell activity, produce metabolites that influence immune responses, and control the release of cytokines and chemokines.
The cryo-EM structure of the human ERAD retrotranslocation complex

Endoplasmic reticulum–associated degradation (ERAD) maintains protein homeostasis by retrieving misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol for degradation. The retrotranslocation of misfolded proteins across the ER membrane is an energy-consuming process, with the detailed transportation mechanism still needing clarification. We determined the cryo-EM structures of the hetero-decameric complex formed by the Derlin-1 tetramer and the p97 hexamer. It showed an intriguing asymmetric complex and a putative coordinated squeezing movement in Derlin-1 and p97 parts. With the conformational changes of p97 induced by its ATP hydrolysis activities, the Derlin-1 channel could be torn into a “U” shape with a large opening to the lipidic environment, thereby forming an entry for the substrates in the ER membrane. The EM analysis showed that p97 formed a functional protein complex with Derlin-1, revealing the coupling mechanism between the ERAD retrotranslocation and the ATP hydrolysis activities.
Atomic structure of the open SARS-CoV-2 E viroporin

The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E’s transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
Red-ox speciation and mixing state of iron in individual African dust particles

[1] The Fe distribution in African dust particles collected in Senegal (North-Western Africa) during the African Monsoon Multidisciplinary Analysis Special Observation Period 0 (AMMA-“SOP 0,” February 2006) was assessed using individual particle analysis (Scanning and Transmission Electron Microscopy respectively equipped with X-ray Spectrometry (SEM-EDX) and Electron Energy Loss Spectrometry (TEM-EELS)). Senegal is not a dust source area; the chemical composition of collected dusts indicates that they originate primarily in the North-Western Sahara, which is consistent with previous studies of the area. Fe can be present inside dust particles as a substitution element in the crystalline lattice of aluminosilicate, but a high proportion (62%) of aluminosilicate Fe-containing particles are also found as an internal mixture of aluminosilicate with Fe oxide grains (including both oxide and hydroxide species). The 3D structure of such particles obtained by tomography reveals that these Fe-rich inclusions are often found at the surface of aluminosilicate particles but that some are also included inside particles. These Fe oxide grains can result from crustal earth or atmospheric processes during long-range transport. FeIII is dominant in both the aluminosilicate matrix and the Fe oxide grains (FeIII/Σ Fe ratio = 76.8% and 90.0%, respectively, on average), with notable heterogeneities of Fe valence inside grains at a nanometer scale.
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

One of the parental diploid genomes (subgenomes) in an allopolyploid often exhibits higher gene expression levels compared to the other subgenome(s) in the nucleus. However, the genetic basis and deterministic fate of subgenome expression dominance remains poorly understood. We examined the establishment of subgenome expression dominance in six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines over the first ten generations, and uncovered consistent expression dominance patterns that were biased towards the Brassica oleracea ‘C’ subgenome across each of the independent lines and generations. The number and direction of gene dosage changes from homoeologous exchanges (HEs) was highly variable between lines and generations, however, we recovered HE hotspots overlapping with those in multiple natural B. napus cultivars. Additionally, we found a greater number of ‘C’ subgenome regions replacing ‘A’ subgenome regions among resynthesized lines with rapid reduction in pollen counts and viability. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the ‘C’ subgenome in all lines and generations. Gene-interaction network analysis indicated an enrichment for network interactions and several biological functions for ‘C’ subgenome biased pairs, but no enrichment was observed for ‘A’ subgenome biased pairs. These findings demonstrate that “replaying the evolutionary tape” in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. Significance Interspecific hybridization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is “dominant” over the other subgenome(s) including higher gene expression levels. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized allopolyploid Brassica napus lines and investigated subgenome dominance patterns over the first ten generations. We found that the same parental subgenome was consistently more dominantly expressed in all lines and generations. This suggests that subgenome expression dominance is largely predetermined based on differences among the parental diploid genomes. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.
The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications

Many archaea and bacteria have an adaptive immune system known as CRISPR which allows them to recognize and destroy foreign nucleic acid that they have previously encountered. Two CRISPR-associated proteins, Cas1 and Cas2, are required for the acquisition step of adaptation, in which fragments of foreign DNA are incorporated into the host CRISPR locus. Cas1 genes have also been found scattered in several archaeal and bacterial genomes, unassociated with CRISPR loci or other cas proteins. Rather, they are flanked by nearly identical inverted repeats and enclosed within direct repeats, suggesting that these genetic regions might be mobile elements (‘casposons’). To investigate this possibility, we have characterized the in vitro activities of the putative Cas1 transposase (‘casposase’) from Aciduliprofundum boonei. The purified Cas1 casposase can integrate both short oligonucleotides with inverted repeat sequences and a 2.8 kb excised mini-casposon into target DNA. Casposon integration occurs without target specificity and generates 14–15 basepair target site duplications, consistent with those found in casposon host genomes. Thus, Cas1 casposases carry out similar biochemical reactions as the CRISPR Cas1-Cas2 complex but with opposite substrate specificities: casposases integrate specific sequences into random target sites, whereas CRISPR Cas1-Cas2 integrates essentially random sequences into a specific site in the CRISPR locus.
UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics

Abstract Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
An examination of the sensitivity of numerically simulated wildfires to low-level atmospheric stability and moisture, and the consequences for the Haines Index

The Haines Index, an operational fire-weather index introduced in 1988 and based on the observed stability and moisture content of the near-surface atmosphere, has been a useful indicator of the potential for high-risk fires in low wind conditions and flat terrain. The Haines Index is of limited use, however, as a predictor of actual fire behavior. To develop a fire-weather index to predict severe or erratic wildfire behavior, an understanding of how the ambient lower-level atmospheric stability and moisture affects the growth of a wildfire is needed. This study is a first step in this process. This study investigates, through four comparative numerical simulations with a coupled wildfire-atmosphere model, the sensitivity of wildland fires to atmospheric stability and moisture, and in the process explores the correspondence between atmospheric stability and moisture, wildfire behavior, and the Haines Index. In the first three fire simulations, the model atmosphere was initially set to identical moisture but different instability conditions that correspond to Haines Indexes for low, moderate, and high potential for severe fire development. In the fourth fire simulation, the initial atmospheric and moisture conditions were for a high-risk fire Haines Index rating, but different from the initial conditions of dryness and stability of the previous experiments. The study indicates that high-risk fire development is sensitive to near-surface atmospheric stability and moisture, and that there is a range of atmospheric stability and moisture conditions that is important to the development of severe or erratic fire behavior, and that this range is within the atmospheric stability and moisture conditions represented by a Haines Index for high potential for severe fire. The analyses also suggest that there is a substantial latitude of fire behavior for fires rated as this Index, indicating that this Index should be further divided, or refined.
DUF916 and DUF3324 in the WxL protein cluster bind to WxL and link bacterial and host surfaces

Bacterial WxL proteins contain peptidoglycan‐binding WxL domains, which have a dual Trp‐x‐Leu motif and are involved in virulence. It was recently shown that WxL proteins occur in gene clusters, containing typically a small WxL protein (which in the mature protein consists only of a WxL domain), a large WxL protein (which contains a C‐terminal WxL domain with N‐terminal host‐binding domains), and a conserved protein annotated as a Domain of Unknown Function (DUF). Here we analyze this DUF and show that it contains two tandem domains—DUF916 and DUF3324—which both have an IgG‐like fold and together form a single functional unit, connected to a C‐terminal transmembrane helix. DUF3324 is a stable domain, while DUF916 is less stable and is likely to require a stabilizing interaction with WxL. The protein is suggested to have an important role to bind and stabilize WxL on the peptidoglycan surface, via the DUF916 domain, and to bind to host cells via the DUF3324 domain. AlphaFold2 predicts that a β‐hairpin strand from DUF916 inserts into WxL adjacent to its N‐terminus. We therefore propose to rename the DUF916‐DUF3324 pair as WxL Interacting Protein (WxLIP), with DUF916, DUF3324 and the transmembrane helix forming the first, second and third domains of WxLIP, which we characterize as peptidoglycan binding domain (PGBD), host binding domain (HBD), and transmembrane helix (TMH) respectively.