Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal Roosting Habits and Population Structure of the Long-fingered Bat Myotis capaccinii in Greece

Abstract The long-fingered bat Myotis capaccinii (Bonaparte, 1837) is considered rare and is listed as vulnerable on the IUCN Red List of Threatened Species (2007). It remains one of the least studied bats in Europe. Protection of roosts is fundamental to bat conservation but, for it to be effective, knowledge about roosting ecology is required. We evaluated roosting habits, colony structure, and colony composition of M. capaccinii in the National Park of Dadia–Lefkimi–Soufli in Greece during 2002–2004 at 6 underground sites. We report results from regular capture of marked individuals and measures of roost microclimate. Individuals formed large maternity colonies in spring. Parturition began in April and by the end of May all captured females had given birth. The 1st volant young appeared in late June and almost all were weaned by the end of July. Summer colonies were sexually segregated; few males were present in the nursery roosts. Adult females began to disperse in August and the proportion of males increased through September and October. Young born in the year remained in the roosts after the females had left. M. capaccinii selected summer roosts with a wide range of temperatures, tolerating temperatures as low as 11.2°C, probably because of the thermoregulatory benefits of aggregating in single- and multispecies clusters. Few individuals remained in these sites during the winter. The majority of females appeared to reach sexual maturity in their 1st autumn and most males did so in their 2nd year. Body mass of males increased steadily from spring through to autumn, whereas mass of females only increased in the autumn before hibernation, except for the additional weight of the fetus during pregnancy, implying that reproduction imposes energetic constraints on females.
CoMask: Corresponding Mask-Based End-to-End Extrinsic Calibration of the Camera and LiDAR

The integration of the camera and LiDAR has played an important role in the field of autonomous driving, for example in visual–LiDAR SLAM and 3D environment fusion perception, which rely on precise geometrical extrinsic calibration. In this paper, we proposed a fully automatic end-to-end method based on the 3D–2D corresponding mask (CoMask) to directly estimate the extrinsic parameters with high precision. Simple subtraction was applied to extract the candidate point cluster from the complex background, and then 3D LiDAR points located on checkerboard were selected and refined by spatial growth clustering. Once the distance transform of 2D checkerboard mask was generated, the extrinsic calibration of the two sensors could be converted to 3D–2D mask correspondence alignment. A simple but efficient strategy combining the genetic algorithm with the Levenberg–Marquardt method was used to solve the optimization problem globally without any initial estimates. Both simulated and realistic experiments showed that the proposed method could obtain accurate results without manual intervention, special environment setups, or prior initial parameters. Compared with the state of the art, our method has obvious advantages in accuracy, robustness, and noise resistance. Our code is open-source on GitHub.
Systematic revision of the middle and late devonian brachiopods Schizophoria (Schizophoria) and ‘Schuchertella’ from North America

Synopsis Schizophoria and ’Schuchertella’, two common genera of Devonian brachiopods from North America, are systematically revised based on cladistic analysis. Several Early Devonian schizo‐phoriid species are placed within S. (Eoschuchertella), while all other North American Devonian and Mississippian species studied are placed within S. (Schizophoria). Schizophoria meeki Fenton & Fenton is synonymised with S. macfarlanii Meek. Ancestral forms of Schizophoria (Schizophoria) were present in Europe and the Appalachian basin and inhabited outer platform environments through the Frasnian. Several independent lineages of S. (Schizophoria) persisted through the Late Devonian biodiversity crisis and subsequently colonised nearshore environments. Most cladogenetic events within North American species of S. (Schizophoria) occurred via dispersal mechanisms, while vicariant speciation was rare. Cladistic analysis of North American species assigned to ’Schuchertella’ revealed that all species through the Frasnian belong to Floweria, an impunctate genus, while Famennian and later species belong to Schuchertella. The generic placement of the Devonian ‘schuchertellids’ is revised accordingly. Schuchertella and Floweria are superficially similar and exhibit an analagous (albeit temporally offset) evolutionary transition from free‐resting ancestors to descendants with attached pedicle valves. Floweria also exhibits reduced rates of vicariant speciation compared to speciation by dispersal. The relative reduction in vicariant speciation has been documented for other Devonian taxa (bivalves, phyllocarids and trilobites) and may be an important control on faunal dynamics in North America during the Late Devonian biodiversity crisis.
The Helicobacter pylori UreI Protein Is Not Involved in Urease Activity but Is Essential for Bacterial Survival In Vivo

ABSTRACT We produced defined isogenic Helicobacter pylori ureImutants to investigate the function of UreI, the product of one of the genes of the urease cluster. The insertion of a catcassette had a strong polar effect on the expression of the downstream urease genes, resulting in very weak urease activity. Urease activity, measured in vitro, was normal in a strain in which ureI was almost completely deleted and replaced with a nonpolar cassette. In contrast to previous reports, we thus found that the product ofureI was not necessary for the synthesis of active urease. Experiments with the mouse-adapted H. pylori SS1 strain carrying the nonpolar ureI deletion showed that UreI is essential for H. pylori survival in vivo and/or colonization of the mouse stomach. The replacement of ureIwith the nonpolar cassette strongly reduced H. pylorisurvival in acidic conditions (1-h incubation in phosphate-buffered saline solution at pH 2.2) in the presence of 10 mM urea. UreI is predicted to be an integral membrane protein and may therefore be involved in a transport process essential for H. pylori survival in vivo.
Assessing the Performance of ICESat-2/ATLAS Multi-Channel Photon Data for Estimating Ground Topography in Forested Terrain

As a continuation of Ice, Cloud, and Land Elevation Satellite-1 (ICESat-1), the ICESat-2/Advanced Topographic Laser Altimeter System (ATLAS) employs a micro-pulse multi-beam photon counting approach to produce photon data for measuring global terrain. Few studies have assessed the accuracy of different ATLAS channels in retrieving ground topography in forested terrain. This study aims to assess the accuracy of measuring ground topography in forested terrain using different ATLAS channels and the correlation between laser intensity parameters, laser pointing angle parameters, and elevation error. The accuracy of ground topography measured by the ATLAS footprints is evaluated by comparing the derived Digital Terrain Model (DTM) from the ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products with that from the airborne Light Detection And Ranging (LiDAR). Results show that the ATLAS product performed well in the study area at all laser intensities and laser pointing angles, and correlations were found between the ATLAS DTM and airborne LiDAR DTM (coefficient of determination––R2 = 1.00, root mean squared error––RMSE = 0.75 m). Considering different laser intensities, there is a significant correlation between the tx_pulse_energy parameter and elevation error. With different laser pointing angles, there is no significant correlation between the tx_pulse_skew_est, tx_pulse_width_lower, tx_pulse_width_upper parameters and the elevation error.
Validation of Sentinel-3A/3B and Jason-3 Altimeter Wind Speeds and Significant Wave Heights Using Buoy and ASCAT Data

This study validated wind speed (WS) and significant wave height (SWH) retrievals from the Sentinel-3A/3B and Jason-3 altimeters for the period of data beginning 31 October 2019 (to 18 September 2019 for Jason-3) using moored buoy data and satellite Meteorological Operational Satellite Program (MetOp-A/B) Advanced Scatterometer (ASCAT) data. The spatial and temporal scales of the collocated data were 25 km and 30 min, respectively. The statistical metrics of root mean square error (RMSE), bias, correlation coefficient (R), and scatter index (SI) were used to validate the WS and SWH accuracy. Validation of WS against moored buoy data indicated errors of 1.19 m/s, 1.13 m/s and 1.29 m/s for Sentinel-3A, Sentinel-3B and Jason-3, respectively. The accuracy of Sentinel-3A/3B WS is better than that of Jason-3. All three altimeters underestimated WS slightly in comparison with the buoy data. Errors in WS at different speeds or SWHs increased slightly as WS or SWH increased. Over time, the accuracy of the Jason-3 altimeter-derived WS improved, whereas that of Sentinel-3A showed no temporal dependence. The WSs of the three altimeters were compared with ASCAT wind data for validation purposes over the global ocean without in situ measurements. On average, the WSs of the three altimeters were lower in comparison with the ASCAT data. The accuracy of the three altimeters was found to be consistent and stable at low/medium speeds but it decreased when the WS exceeded 15 m/s. Validations of SWH against buoy wave data indicated that the accuracy of Jason-3 SWH was better than that of Sentinel-3A/3B. However, the accuracy of all three altimeters decreased when the SWH exceeded 4 m. The accuracy of Sentinel-3A and Jason-3 SWH was temporally stable, whereas that of Sentinel-3B SWH improved over time. Analyses of SWH accuracy as a function of wave period showed that the Jason-3 altimeter was better than the Sentinel-3A/3B altimeters for long-period ocean waves. Generally, the accuracy of WS and SWH data derived by the Sentinel-3A/3B and Jason-3 altimeters satisfies their mission requirements. Overall, the accuracy of WS (SWH) derived by Sentinel-3A/3B (Jason-3) is better than that retrieved by Jason-3 (Sentinel-3A/3B).
The IFITM Proteins Inhibit HIV-1 Infection

The IFITM Proteins Inhibit HIV-1 Infection Jennifer Lu, Qinghua Pan, Liwei Rong, Wei He, Shan-Lu Liu, and Chen Liang McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2; and Department of Medicine and Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada H3A 2B4; and Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310
Characterization of thep-Toluenesulfonate OperontsaMBCD andtsaRinComamonas testosteroniT-2

Comamonas testosteroni T-2 uses a standard, if seldom examined, attack on an aromatic compound and oxygenates the side chain ofp-toluenesulfonate (TS) (orp-toluenecarboxylate) top-sulfobenzoate (or tereph- thalate) prior to complete oxidation. The expression of thefirst three catabolic enzymes in the pathway, the TS methyl-monooxygenase system (comprising reductase B and oxygenase M; TsaMB), p-sulfobenzyl alcohol dehydrogenase (TsaC), andp-sulfobenzaldehyde dehydrogenase (TsaD), is coregulated as regulatory unit R1 (H. R. Schlafli Oppenberg, G. Chen, T. Leisinger, and A. M. Cook, Microbiology (Reading) 141:1891-1899, 1995). Thecomponentsoftheoxygenasesystemwererepurified,andtheN-terminalaminoacidsequenceswere confirmed and extended. An internal sequence of TsaM was obtained, and the identity of the (2Fe-2S) Rieske center was confirmed by electron paramagnetic resonance spectroscopy. We purified both dehydrogenases (TsaC and TsaD) and determined their molecular weights and N-terminal amino acid sequences. Oligonucle- otidesderivedfromthepartialsequencesofTsaMwereusedtoidentifyclonedDNAfromstrainT-2,andabout 6 kb of contiguous cloned DNA was sequenced. Regulatory unit R1 was presumed to represent a four-gene operon (tsaMBCD) which was regulated by the LysR-type regulator, TsaR, encoded by a deduced one-gene transcriptional unit. The genes for the inducible TS transport system were not at this locus. The oxygenase system was confirmed to be a class IA mononuclear iron oxygenase, and class IA can now be seen to have two evolutionary groups, the monooxygenases and the dioxygenases, though the divergence is limited to the oxygenase components. The alcohol dehydrogenase TsaC was confirmed to belong to the short-chain, zinc- independent dehydrogenases, and the aldehyde dehydrogenase TsaD was found to resemble several other aldehyde dehydrogenases. The operon and its putative regulator are compared with units of the TOL plasmid.
Selecting indicator traits for monitoring land use impacts: Birds in northern coastal birch forests

Coastal birch forests in northern Norway are currently being converted to nonnative spruce plantations. Since such land use changes may cause large alterations in the birch forest ecosystems, indicators suitable for detecting and monitoring impacts need to be pursued. In this study, we used a three-table ordination method (RLQ analysis) to identify species traits in bird assemblages indicating changes in environmental attributes at stand and landscape level. RLQ analysis has the advantage of linking species traits directly to environmental attributes, hence detecting the major ecological impacts of land use change, as well as a set of species traits sensitive to these alterations. Birds and environmental attributes were sampled in six forest types in 12 different landscapes. To assess whether species traits were relatively consistent geographically and temporally, two different geographic regions and years were also included in our study design. We found the species traits investigated here to be promisin.
Effects of experimental food provisioning on reproduction in the Jackdaw Corvus monedula, a semi‐colonial species

Two Jackdaw Corvus monedula colonies were given supplementary food before and during breeding in 1983. Breeding density and cavity use were compared with those of the same colonies in previous years, when no food was provided. Predation rate and reproductive parameters were compared with those in the same colonies in previous years and with those of two control colonies, without experimental food. Jackdaws preferred safe cavities with small minimum nest-entrance dimensions and avoided those with a high risk of nest predation. In experimental (fed) colonies, however, there was a tendency to use all cavities, which resulted in an increased breeding density. No nests were preyed upon by Ravens Corvus corax in the experimental colonies because supplemental food favoured group defence by increasing colony size and by increasing the time the Jackdaws spent in the colony. Additional food advanced laying date, increased clutch size independently of laying date and increased fledging success. Supplementary food significantly increased fledging success in less than half of all experimental studies on birds. We suggest that the key to this problem is the species' breeding strategy, and we show that supplementary food significantly increased fledging success in brood-reduction strategist species but not in species which directly adjusted their clutch size.
MECHANICS OF MODEL BUILDING

In the late 1960s, with the advent of wide availability of the digital computer, it became possible by applying systems theory to build simulation models of biological entities. In production agriculture, scientists have built models for various field crops: cotton ( Gossypium hirsutum L.), corn (Zea mays L.), wheat (Triticum aestivum L.), soybean [Glycine max (L.) Merr. ], and alfalfa ( Medicago sativa L.). In most of the models built to date, crop phenology is simulated directly with detailed aspects of crop physiology. Some models also rely on principles of soil physics to some degree. This paper addresses the methodology of constructing process-level, physiologically based crop simulation models that possess detailed descriptions of plant physiological and soil physical mechanisms and proposes a minimum set of design features. THE DATABASE Data availability largely determines the type of model of a physiological process, or an entire crop, that a modeler can develop. Unfortunately, most field-crop experiments are designed to determine either differences between means or the significance of specific treatments, not an understanding of the cause of treatment differences. As a result, one cannot determine from field data which external events caused responses in the biological‐physical system. If a model is developed from such a data set, that model will be valid only for data conditions at that site for the years over which the data were collected and cannot reliably be extended to other sites or other years. In a simulation model, detailed information must be available on all exogenous variables that can affect the process or crop being studied. For example, if one were modeling leaf growth and development, many variables would have to be known to build a comprehensive leaf model: date the leaf was initiated and the change in leaf size, N concentration, water potential, temperature, exposure to solar radiation, dry weight, stomatal conductance, and photosynthesis rate. Of course, most of these variables would have to be measured from leaf initiation through senescence. If significant information is missing from this data set, the type of model one can construct is limited. If temperature data were missing, the job would become very difficult. If leaf N concentration data are missing, a leaf model could be built, but the model would be confounded by the unknown leaf N status under which the data set was collected. In applying systems methodology to modeling biological systems, experiments are designed to determine cause and effect and measure external variables pertinent to the system being studied. Even when one strives to be comprehensive in field research experiments, certain classes of experiments cannot be conducted in the field. For example,
Identification of molecular marker linked to stem rust resistance gene in synthetic hexapolid lines of wheat (Triticum aestvium L.)

In order to enrich the molecular markers linked to wheat stem rust resistance gene and to facilitate the marker-assisted selection in breeding programme, bulk segregation analysis was carried out for gene tagging using F2 segregating population derived from cross between wheat synthetic 4 line with resistant gene (Sr gene carrier) and a common wheat variety Agra local (susceptible to wheat stem rust). This Sr gene carrier synthetic 4 was derived between a cross Triticum turgidum (AABB) and Triticum tauschii (DD). A total of 35 SSR primers covering D and B Genome on the basis of chromosomal location of resistance genes were screened. The SSR marker namely Xgwon106, Xgwm432, Xgwm533 and Xgwm369 have revealed polymorphism among the parents used for study. The SSR Xgwm 533 was found to be putative linked with stem rust resistance gene while the marker Xgwm 389 was co- segregating with Xgwm 533. Marker Xgwm 533 and Xgwm 389 were taken from B genome. Hence, the stem rust resistance gene presumed to be located on 3-B genome of wheat. The use of these markers in combination with others markers could better predict the presence of stem rust resistance gene in wheat genome. Key words: Stem rust (Puccinia graminis f.sp. tritici), molecular tagging, bulk segregation analysis, synthetic hexaploid wheat, SSR primers.
Quantification of Precipitation Using Polarimetric Radar Measurements during Several Typhoon Events in Southern China

Accurate quantitative precipitation estimation (QPE) during typhoon events is critical for flood warning and emergency management. Dual-polarization radar has proven to have better performance for QPE, compared to traditional single-polarization radar. However, polarimetric radar applications have not been extensively investigated in China, especially during extreme events such as typhoons, since the operational dual-polarization system upgrade only happened recently. This paper extends a polarimetric radar rainfall system for local applications during typhoons in southern China and conducts comprehensive studies about QPE and precipitation microphysics. Observations from S-band dual-polarization radar in Guangdong Province during three typhoon events in 2017 are examined to demonstrate the enhanced radar rainfall performance. The microphysical properties of hydrometeors during typhoon events are analyzed through raindrop size distribution (DSD) data and polarimetric radar measurements. The stratiform precipitation in typhoons presents lower mean raindrop diameter and lower raindrop concentration than that of the convection precipitation. The rainfall estimates from the adapted radar rainfall algorithm agree well with rainfall measurements from rain gauges. Using the rain gauge data as references, the maximum normalized mean bias ( N M B ) of the adapted radar rainfall algorithm is 20.27%; the normalized standard error ( N S E ) is less than 40%; and the Pearson’s correlation coefficient ( C C ) is higher than 0.92. For the three typhoon events combined, the N S E and N M B are 36.66% and -15.78%, respectively. Compared with several conventional radar rainfall algorithms, the adapted algorithm based on local rainfall microphysics has the best performance in southern China.
Effects of Herbicides on Italian Ryegrass (Lolium multiflorum), Forage Production, and Economic Returns from Dual-Purpose Winter Wheat (Triticum aestivum)1

Abstract: Two field experiments were conducted to evaluate the effects of selected herbicides on Italian ryegrass, combined Italian ryegrass plus wheat forage production, and returns from hard red winter wheat grain. Herbicides included BAY FOE 5043 + metribuzin (4:1 w/w premix), BAY MKH 6562, chlorsulfuron, chlorsulfuron + metsulfuron (5:1 w/w premix), diclofop, MON 37560, pendimethalin, ICIA 0604, and triasulfuron. Italian ryegrass was controlled 80% or more by 28 of 34 treatments. Grain dockage was reduced by 33 of 34 treatments at both sites, and grain yield was improved at both sites by 29 of 34 treatments. No herbicide treatment decreased forage protein content, but forage yield was frequently decreased by controlling Italian ryegrass. Gross returns from wheat grain were improved over the untreated check by all but six treatments at site 1, and by all but one treatment at site 2. The data did not support the hypothesis that returns from forage plus grain could be maximized by delaying Italian ryegrass control until grazing termination. Nomenclature: BAY FOE 5043, N-(4-fluorophenyl)-N-(1-methylethyl)-2-[[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]oxy]acetamide; BAY MKH 6562, 1H-1,2,4-triazole-carboxamide,4,5-dihydro-3-methoxy-4-methyl-5-oxo-N-[[2-(trifluoromethoxy)phenyl]sulfonyl]-sodium salt; chlorsulfuron; diclofop; metribuzin; metsulfuron; MON 37560, 1-(4,6-dimethoxypyrimidin-2-yl)-3-[(ethanesulfonyl-imidazo[1,2-a]-pyridine-3-yl)sulfonyl]urea; pendimethalin; ICIA 0604 (proposed common name, tralkoxydim), 2-cyclohexen-1-one,2-[1-(ethoxyimino)propyl]-3-hydroxy-5-(2,4,6-trimethylphenyl)-(9Cl); triasulfuron; Italian ryegrass, Lolium multiflorum Lam. , Marshall #3 LOLMU; wheat, Triticum aestivum L. , 2137. Additional index words: BAY FOE 5043, BAY MKH 6562, chlorsulfuron, diclofop, metribuzin, metsulfuron, MON 37560, pendimethalin, ICIA 0604, triasulfuron, forage. Abbreviations: DAS, days after seeding; POST, postemergence; PRE, preemergence.