bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic microbiome assembly depends on context
Authors: Jones Eric W. , Carlson Jean M. , Sivak David A. , Ludington William B. 
Published: February 2022

Significance
Individuals are constantly exposed to microbial organisms that may or may not colonize their gut microbiome, and newborn individuals assemble their microbiomes through a number of these acquisition events. Since microbiome composition has been shown to influence host physiology, a mechanistic understanding of community assembly has potentially therapeutic applications. In this paper we study microbiome acquisition in a highly controlled setting using germ-free fruit flies inoculated with specific bacterial species at known abundances. Our approach revealed that acquisition events are stochastic, and the colonization odds of different species in different contexts encode ecological information about interactions. These findings have consequences for microbiome-based therapies like fecal microbiota transplantation that attempt to modify a person’s gut microbiome by deliberately introducing foreign microbes.
Munc13 structural transitions and oligomers that may choreograph successive stages in vesicle priming for neurotransmitter release
Authors: Grushin Kirill , Kalyana Sundaram R. Venkat , Sindelar Charles V. , Rothman James E. 
Published: February 2022

Significance
The speed of neural information processing in the human central nervous system is ultimately determined by the speed of chemical transmission at synapses, because action potentials have relatively short distances to traverse. The release of synaptic vesicles containing neurotransmitters must therefore be remarkably fast as compared to other forms of membrane fusion. Six separate SNARE complexes cooperate to achieve this. But how can exactly six copies be assembled under every vesicle? Here we report that six copies of the key molecular chaperone that assembles the SNAREs can arrange themselves into a closed hexagon, providing the likely answer.
A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics
Authors: Karmi Ola , Marjault Henri-Baptiste , Bai Fang , Roy Susmita , Sohn Yang-Sung , Darash Yahana Merav , Morcos Faruck , Ioannidis Konstantinos , Nahmias Yaakov , Jennings Patricia A. , Mittler Ron , Onuchic José N. , Nechushtai Rachel 
Published: February 2022

SignificanceHere we address the important question of cross-talk between the mitochondria and cytosol. We show that the inner mitochondrial protein, MiNT, interacts with a protein on the outer mitochondrial membrane (mNT). This interaction occurs within the major outer membrane protein VDAC1. Inside the inner space of VDAC1, MiNT transfers its [2Fe-2S] clusters to mNT, which was shown to be a [2Fe-2S] cluster donor protein that donates its cluster(s) to apo-acceptor proteins residing in the cytosol. Hence, we suggest a pathway for transferring [2Fe-2S] clusters from inside the mitochondria to the cytosol.
Functional network topography of the medial entorhinal cortex
Authors: Obenhaus Horst A. , Zong Weijian , Jacobsen R. Irene , Rose Tobias , Donato Flavio , Chen Liangyi , Cheng Heping , Bonhoeffer Tobias , Moser May-Britt , Moser Edvard I. 
Published: February 2022

Significance
The investigation of the topographic organization of spatially coding cell types in the medial entorhinal cortex (MEC) has so far been held back by the lack of appropriate tools that enable the precise recording of both the anatomical location and activity of large populations of cells while animals forage in open environments. In this study, we use the newest generation of head-mounted, miniaturized two-photon microscopes to image grid, head-direction, border, as well as object-vector cells in MEC and neighboring parasubiculum within the same animals. The majority of cell types were intermingled, but grid and object-vector cells exhibited little overlap. The results have implications for network models of spatial coding.
Towards a taxonomy of arguments for and against street renaming
Authors: Buchstaller Isabelle , Schneider Carolin , Alvanides Seraphim 
Published: February 2022

Abstract
In 2016, a special issue of the Linguistic Landscapes: An International Journal explored the nexus between LL and collective memory studies, calling for more research at the interface of these disciplines. Our analysis adds to recent studies by exploring the ways in which commemorative street renaming processes are discursively embedded. We build on research on memorialisation as well as critical toponymy to analyse media discourses that accompany, support or contest commemorative naming practices in the urban streetscape of a large East German city during the last century. Based on this dataset, we develop a typology of arguments against or in favour of street renaming. The longitudinal analysis of discourses in the local press vis-à-vis ongoing resemioticisation reveals a complex relationship between lived political history, freedom of the press, the type of argument and the stances encoded therein.
Inflation and the cosmological (not-so) constant in unimodular gravity
Authors: León Gabriel 
Published: February 2022

Abstract
We propose a mechanism for generating an inflationary phase in the early universe without resorting to any type of scalar field(s). Instead, this accelerated expansion is driven by a dynamical ‘cosmological constant (CC)’ in the framework of unimodular gravity (UG). The time dependent CC can be related to an energy diffusion term that arises naturally in UG due to its restrictive diffeomorphism invariance. We derive the generic conditions required for any type of diffusion to generate a realistic inflationary epoch. Furthermore, for a given parameterization of inflation (in terms of the Hubble flow functions), we show how to construct the corresponding diffusion term in such a way that a smooth transition occurs between inflation and the subsequent radiation dominated era, hence reheating proceeds naturally. The primordial spectrum is obtained during the inflationary phase by considering inhomogeneous perturbations associated to standard hydrodynamical matter (modeled as a single ultra-relativistic fluid). We demonstrate that the resulting spectrum is equivalent to that obtained in traditional inflationary models, and is also independent of the particular form of the diffusion term. In addition, we analyze the feasibility of identifying the variable CC, responsible for the inflationary expansion, with the current observed value.
Short-range organization and photophysical properties of CdSe quantum dots coupled with aryleneethynylenes
Authors: Theurer Christoph P , Weber Antonia , Richter Martin , Bender Markus , Michel Patrick , Rana Debkumar , Kumar Krishan , Bunz Uwe , Scheele Marcus , Tegeder Petra , Schreiber Frank , Broch Katharina 
Published: February 2022

Abstract
Hybrid organic–inorganic nanomaterials composed of organic semiconductors and inorganic quantum dots (QDs) are promising candidates for opto-electronic devices in a sustainable internet of things. Especially their ability to combine the advantages of both compounds in one material with new functionality, the energy-efficient production possibility and the applicability in thin films with little resource consumption are key benefits of these materials. However, a major challenge one is facing for these hybrid materials is the lack of a detailed understanding of the organic–inorganic interface which hampers the widespread application in devices. We advance the understanding of this interface by studying the short-range organization and binding motif of aryleneethynylenes coupled to CdSe QDs as an example system with various experimental methods. Clear evidence for an incorporation of the organic ligands in between the inorganic QDs is found, and polarization-modulation infrared reflection-absorption spectroscopy is shown to be a powerful technique to directly detect the binding in such hybrid thin-film systems. A monodentate binding and a connection of neighboring QDs by the aryleneethynylene molecules is identified. Using steady-state and time resolved spectroscopy, we further investigated the photophysics of these hybrid systems. Different passivation capabilities resulting in different decay dynamics of the QDs turned out to be the main influence of the ligands on the photophysics.
Germanium thin film manufacturing using covalent bonding process
Authors: Abadie K , Fournel F , Morales C , Mazen F , Vignoud L , Colonna J-P , Widiez J 
Published: February 2022

Abstract
This article deals with Si/Ge heterostucture manufacturing using covalent bonding, and its application to the layer transfer of a thin germanium film. At first, bow simulations of the heterostructure are discussed, in order to determine the temperature that should be used during bonding. Then, the covalent bonding process used to manufacture the heterostructure is described and characterized. At the end, a layer transfer process and observations of a thin germanium film are presented.
Emergent magnonic singularities in anti parity-time symmetric synthetic antiferromagnets
Authors: Sui Chao-Wei , Yuan Shao-Hua , Wang Xi-Guang , Berakdar Jamal , Jia Chenglong 
Published: February 2022

Abstract
We study the impact of the transition across the anti-parity-time (anti-

PT

) symmetry breaking point on the low-energy spin excitations in a synthetic antiferromagnet (SyAFM) that consists of two magnetic layers coupled antiferromagnetically via the Ruderman–Kittel–Kasuya–Yosida (RKKY) interaction. When varying the interlayer (RKKY) coupling strength a degeneracy point (exceptional point) is reached beyond which the system enters the anti-

PT

symmetry-broken phase. This phase is marked by the emergence of a finite net magnetization and low-lying excitations beyond the Goldstone modes in the anti-

PT

symmetry-preserved phase. For systems hosting an interfacial Dzyaloshinskii–Moriya interaction, we find a bound state in the continuum with a maximal coherent superposition of SyAFM excitations without any radiation. Analytical results for linearized models are corroborated with full numerical micromagnetic simulations endorsing the robustness and generalities of the theory predictions.
Single electron in a storage ring: a probe into the fundamental properties of synchrotron radiation and a powerful diagnostic tool
Authors: Lobach I. , Nagaitsev S. , Romanov A. , Stancari G. 
Published: February 2022

Abstract
An experimental study of undulator radiation generated by a
single electron was carried out at the Integrable Optics Test
Accelerator (IOTA) storage ring at Fermilab. Photons were detected
with a single-photon avalanche diode (SPAD) at an average rate of
20 kHz, corresponding to one detection every few hundred
revolutions. Events were continuously recorded by a picosecond event
timer for as long as 5 minutes at a time. The collected data were
used to directly test the predictions of classical Poisson
photostatistics. The study was motivated in part by a previous
observation of sub-Poissonian statistics in a similar experiment
with synchrotron radiation. In addition, we show that the time
series of recorded events can be used to study the synchrotron
motion of a single electron, yielding dynamical parameters such as
the phase jitter of the radiofrequency cavity and the dependence of
the synchrotron period on amplitude. Research plans for further
experiments are also discussed.
Concept of a fast neutron detector based on 10B-RPCs
Authors: Morozov A. , Margato L.M.S. , Blanco A. , Galaviz D. 
Published: February 2022

Abstract
We propose an alternative approach for the detection of fast
neutrons in the energy range from 10-4 to 5 MeV based on
10B-RPCs (hybrid double-gap Resistive Plate Chambers with
10B4C neutron converters) surrounded by a polyethylene
moderator. The detection efficiency as a function of the neutron
energy is obtained in Monte Carlo simulations performed with the
Geant4 toolkit for several detector configurations. The thickness of
the neutron converter is optimized for the maximum efficiency. The
results show that for this type of detector it is possible to obtain
an average detection efficiency larger than 50% with a weak
dependence on the neutron energy. The dark count rate and gamma
sensitivity are also discussed.
Reconstructing global PM2.5 monitoring dataset from OpenAQ using a two-step spatio-temporal model based on SES-IDW and LSTM
Authors: Tan Siyu , Wang Yuan , Yuan Qiangqiang , Zheng Li , Li Tongwen , Shen Huanfeng , Zhang LiangPei 
Published: February 2022

Abstract
Fine particulate matter (PM2.5) is widely concerned for its harmful impacts on global environment and human health, making air pollution monitoring so crucial and indispensable. As the world’s first open, real-time, and historical air quality platform, OpenAQ collects and provides government measurement and research-level data from various channels. However, despite OpenAQ’s innovation in providing us with ground-measured PM2.5 worldwide, we find significant data gaps in time series for most of the sites. The incompleteness of the data directly affects the public perception of PM2.5 concentration levels and hinders the progress of research related to air pollution. To address these issues, a two-step hybrid model named ST-SILM, i.e. spatio-temporal model with single exponential smoothing-inverse distance weighted (SES-IDW) and long short-term memory (LSTM), is proposed to repair the missing data from PM2.5 sites worldwide collected from OpenAQ from 2017 to 2019. Both spatio-temporal correlation and neighborhood fields are considered and established in the model. To be specific, SES-IDW were firstly used to repair missing values, and secondly, the LSTM network was employed to reconstruct the time series of continuous missing data. After the global ground-measured PM2.5 was reconstructed, the light gradient boosting machine model was applied to remote sensing estimation of the original ground-measured PM2.5 and of the reconstructed ground-measured PM2.5 to further verify the performance of ST-SILM. Experiment results show that the estimation accuracy of the reconstructed dataset is better (R
2 from 2017 to 2019 increased by 0.02, 0.02, and 0.01 compared with the original dataset). Therefore, it is concluded that the proposed model can effectively reconstruct data from PM2.5 sites worldwide.
Beyond thermodynamic uncertainty relations: nonlinear response, error-dissipation trade-offs, and speed limits
Authors: Falasco Gianmaria , Esposito Massimiliano , Delvenne Jean-Charles 
Published: February 2022

Abstract
From a recent geometric generalization of thermodynamic uncertainty relations (TURs) we derive novel upper bounds on the nonlinear response of an observable of an arbitrary system undergoing a change of probabilistic state. Various relaxations of these bounds allow to recover well known bounds such as (strengthenings of) Cramer–Rao’s and Pinsker’s inequalities. In particular we obtain a master inequality, named symmetric response intensity relation, which recovers several TURs as particular cases. We employ this set of bounds for three physical applications. First, we derive a trade-off between thermodynamic cost (dissipated free energy) and reliability of systems switching instantly between two states, such as one-bit memories. We derive in particular a lower bound of 2.8k
B
T per Shannon bit to write a bit in such a memory, a bound distinct from Landauer’s one. Second, we obtain a new family of classic speed limits which provide lower bounds for non-autonomous Markov processes on the time needed to transition between two probabilistic states in terms of a thermodynamic quantity (e.g. non-equilibrium free energy) and a kinetic quantity (e.g. dynamical activity). Third, we provide an upper bound on the nonlinear response of a system based solely on the ‘complexity’ of the system (which we relate to a high entropy and non-uniformity of the probabilities). We find that ‘complex’ models (e.g. with many states) are necessarily fragile to some perturbations, while simple systems are robust, in that they display a low response to arbitrary perturbations.
In silico restriction site analysis for characterization of Toxoplasma gondii isolate
Authors: Ekawasti F , Cahyaningsih U , Sadi’ah S , Dharmayanti N L P I , Subekti D T 
Published: February 2022

AbstractToxoplasma gondiiinfection is a serious major public health concern. Toxoplasmosis is a disease that affects humans and warm-blooded animals all over the world. The virulence and severity of the sickness may be influenced by parasite load. The three clonal lineages for biological research areT. gondiigenotypes I, II, and III. Using primer genes forgra1, rop1, andmic3, which have been identified as essential proteins for tachyzoite invasion and replication in host cells. PCR was used to determine the genotype of aT. gondiiisolate from the Indonesian research center for veterinary science.In silicorestriction site analysis was performed onT. gondiiisolates using CLC sequence viewer 8.0 software to assess sequence data for the existence of restriction enzyme patterns. Predictable restriction fragment length polymorphism usingIn silicoanalysis.T. gondiisequencing genes areIn silicodigested with different restriction enzymes. The findings show that they can easily distinguish archetypal parasites from biotypes and estimate the genetic diversity of the parasites. According to the interpretation of the data, isolateT. gondiibelongs to strain RH genotype I.
Surgical removal of bladder stone in a sulcata tortoise (Centrochelys sulcata): A case study
Authors: Raharjo S , Widyarini S , Indarjulianto S , Yanuartono  
Published: February 2022

Abstract
A 2 years old male sulcata (Centrochelys sulcata) tortoise presented to the clinic with problems of refuse to eat for 2 weeks, weaken, sleeping all day long and no defecated or urinating during last 1 week. The population is 24 tortoises in many species. Daily diets mainly on lettuce and cabbage. Clinical signs found during physical examination were closed eyelids, weakness and inactive. An X-ray imaging was presented and found a large white mass in urinary bladder. The diagnose was bladder stones or calculi vesicalis. Due to the size and the density of the bladder stones, a surgery intervention for bladder stones removal was conducted. Anesthesia using ketamine dose 30 mg/kg BW combine with xylazine dose 2 mg/kg BW injected intramuscularly. The surgery starts with cutting the plastron using a sterile dremel, opening the plastron and put the cutting plastron in saline water, opening the coelomic cavity by incising the abdominal muscles, finding the urinary bladder, incision the urinary bladder, removing the bladder stones, flushing the urinary bladder, suturing the urinary bladder, suturing the abdominal muscles, closing the plastron and applying the epoxy glue for covering the cutting plastron. Antibiotic enrofloxacine 10% with dose 5 mg/kg BW combine with antiinflamatory tolfenamic acid 4% and vitamin B complex all are injected intramuscularly once a day for 5 consecutive days. The tortoise was hospitalized and monitoring daily. The tortoise recover in day 4 after surgery, start eating and healing to normal activities in day 7.
Daily behavioral activities of the proboscis monkey (Nasalis larvatus Wurmb) in the Bekantan Rescue Center, Sahabat Bekantan Indonesia foundation
Authors: Nurliani A , Rezeki A , Istiqomah S , Rusmiati  , Hoesain F F 
Published: February 2022

Abstract
The proboscis monkey or long-nosed monkey is diurnal and arboreal. This species is endemic to Borneo Island inhabit mangrove forest and swampland. Daily behavioral activities of the proboscis monkey kept in the Bekantan Rescue Center, Sahabat Bekantan Indonesia Foundation was interesting to be observed. A couple of adult proboscis monkey, which was approximately 10 years old for each individu, was utilized in the current study. Observation on daily behavioral activities included locomotion, eating, antagonistic, playing, grooming, and rest-activity. Proboscis monkey spent their daily time for resting, locomotion, grooming, eating, antagonistic, and playing with each percentage were 42.50%; 26.04%; 17.15%; 9.29%; 0.86%; and 0.13%, consecutively. Locomotion activities consisted of walk, jump, moving seat, swing, and cage-shaking. Grooming by removing pieces of dirt, dried skin, and insects from the hair were done individually and more frequently in female than male. Eating activities were 3 times a day, morning, noon, and afternoon with the duration of 5-15 minutes. An antagonistic expression such as opening wide-mouth, vocalization, and cage-shaking was frequently observed in the male shown when the unknown person was present. Playing activity was the lowest percentage activity observed. This activity is less frequently observed in the adult period. Rest activity consisted of night sleep and day sleep. Night sleep was observed from 09.00 P.M to 6.00 A.M, and day sleep was observed after eating time in the morning and noon. Daily behavioral activities of the proboscis monkey in the Bekantan Rescue Center tend to be done routinely and regularly.
Activity test of chitosan haruan (Channa striata) fish scales as antibiofilm agent againts biofilm of Porphyromonas gingivalis
Authors: Putri D K T , Ilham M S , Adhani R , Utami J P , Rahmiati  
Published: February 2022

AbstractBackground:Porphyromonas gingivalishas been known as the major bacterial that induce periodontal inflammation through biofilm formation. Biofilms contain important virulence factors such as lipopolysaccharides. These virulence factors can make it escape from the periodontal immune system and modulate biofilms by increasing tolerance to antibiofilm agents so that biofilm formation becomes uncontrolled. The Chitosan from Haruan (Channa Striata) fish scales contains a degree of deacetylation of 85.25% which is associated with the content of an amine group (-NH2) which is positively charged in the Chitosan haruan fish scale which can act as an antibiofilm. Objective: The aim of this study was to analyze the activity of Chitosan Haruan fish scales (Channa striata) as an antibiofilm agent on Porphyromonas gingivalis biofilms. Methods: The research design used in this study was a true experimental design with a post-test with a control group design using 4 treatments and 1 positive control. All treatments were carried out biofilm testing to obtain Optical Density. Results: The results showed that chitosan Haruan fish scales with a concentration of 2.5%, 10%, 20%, 40% proved to be able to damage the Porphyromonas gingivalis biofilm. Conclusion: Chitosan Haruan fish scales have the ability as an antibiofilm agent against P.gingivalis biofilms.
Comparison of dissolved organic carbon and nutrients content in Papua peatland
Authors: Sundari S 
Published: February 2022

Abstract
Indonesia’s peatlands degrade due to land conversion and land development. Peatland conversion affects nutrient content in peat soil and peat water, including dissolved organic carbon (DOC). Research on the comparison of DOC and nutrient content was conducted in Papua peatland. It was carried out at Kaliki and Marga Mulia in Merauke, and also at Khanami and Yame in Mappi. This research aimed to determine DOC, soil, and water nutrients, then compare them among peatlands in Merauke and Mappi. At each location, three replications of peat water and peat soil were sampled by digging to a depth of 20 cm. The peat water was estimated for DOC concentration and nutrients, but peat soil was analyzed for nutrients only. The DOC concentration at Yame was the highest among the sites, followed by Khanami, Marga Mulia, and Kaliki. Soil carbon stored was estimated highest at Khanami, followed by Kaliki, Yame, and Marga Mulia. It was concluded that the DOC and soil carbon stored were higher in Mappi peatland than in Merauke peatland because it was still preserved by the community and no peatland conversion in Mappi.