Miracle-dz/UniFAR-FTUs huggingface dataset:
A systematic review of neglected tropical diseases (NTDs) in Myanmar

Background Neglected tropical diseases (NTDs) affect most impoverished communities in developing countries, like Myanmar in Southeast Asia. NTDs have been understudied and underreported in Myanmar. Methods A systematic review of published and grey literature (1900–2023) on neglected tropical diseases (NTDs) in Myanmar was conducted. The literature search included five international databases: PubMed, EMBASE, Ovid Global Health, and Web of Science Core Collection and one national database: the Myanmar Central Biomedical Library (locally published papers and grey literature). The selection criteria included articles with all types of study designs of current or previous infections conducted in humans, that reported NTDs, recognised by WHO, US CDC, and listed in PLoS NTDs. We included melioidosis and rickettsioses which we consider also meet the definition of an NTD. Results A total of 5941 records were retrieved and screened, of which, 672 (11%) met the selection criteria and were included in this review. Of the included articles, 449 (65%) were published after 2000 and 369 (55%) were from two regions (Yangon and Mandalay) of Myanmar. Of the included articles, 238 (35%) reported bacterial NTDs, 212 (32%) viral NTDs, 153 (23%) helminth NTDs, 25 (4%) protozoal NTDs and 39 (6%) reported more than one aetiology. Based on reported frequency in descending order, the bacterial NTDs were leprosy, Escherichia coli enteritis, salmonellosis, cholera, shigellosis, melioidosis, leptospirosis and rickettsioses; the viral NTDs were dengue, chikungunya and Japanese encephalitis virus (JEV) infection; the protozoal NTDs were amoebiasis, giardiasis and leishmaniasis, and the helminth NTDs were ascariasis, trichuriasis, hookworm disease, filariasis and strongyloidiasis. Conclusion This review summarises NTDs reported in Myanmar over the past 100 years. The findings suggest that most NTDs are likely to be under reported, especially from the majority of the country which is far from academic centres. Research capacity building together with strengthening of laboratory systems would lead to better understanding of the true burden of NTDs in Myanmar. Trial registration PROSPERO registration ID: CRD42018092627.
Space and time on the membrane: modelling Type VI secretion system dynamics as a state-dependent random walk

The type six secretion system (T6SS) is a transmembrane protein complex that mediates bacterial cell killing. The T6SS comprises three main components (transmembrane, baseplate and sheath/tube complexes) that are sequentially assembled in order to enable an attacking cell to transport payloads into neighbouring cells. A T6SS attack disrupts the function of essential cellular components of target cells, typically resulting in their death. While the assembled T6SS adopts a fixed position in the cell membrane of the attacking cell, the location of the firing site varies between firing events. In Serratia marcescens, a post-translational regulatory network regulates the assembly and firing kinetics of the T6SS in a manner that affects the attacking cell’s ability to kill target cells. Moreover, when the ability of membrane complexes to reorient is reduced, an attacking cell’s competitiveness is also reduced. In this study, we will develop a mathematical model that describes both the spatial motion and assembly/disassembly of a firing T6SS. The model represents the motion of a T6SS on the cell membrane as a state-dependent random walk. Using the model, we will explore how both spatial and temporal effects can combine to give rise to different firing phenotypes. Using parameters inferred from the available literature, we show that variation in estimated diffusion coefficients is sufficient to give rise to either spatially local or global firers.
Effects of wind on convection in strongly and weakly baroclinic flows with application to the Labrador Sea

Abstract Large buoyancy loss driving deep convection is often associated with a large wind stress that is typically omitted in simulations of convection. Here it is shown that this omission is not justified when overturning occurs in a horizontally inhomogeneous ocean. In strongly baroclinic flows, convective mixing is influenced both by the background horizontal density gradient and by the across-front advection of buoyancy due to wind. The former process—known as slantwise convection—results in deeper convection, while the effect of wind depends on the relative orientation of wind with respect to the baroclinic front. For the case of the Labrador Sea, wintertime winds act to destabilize the baroclinic Labrador Current causing a buoyancy removal roughly one-third as large as the air–sea buoyancy loss. Simulations using a nonhydrostatic numerical model, initialized and forced with observed fields from the Labrador Sea, show how the combination of wind and lateral gradients can result in significant convec.
Comparison of Morbidity, Mortality, and Costs of VAP Patients with Non-VAP Patients in the Tertiary Referral Hospital of Kerman, Iran

Background: Ventilator-associated pneumonia is the most common type of nosocomial infection in ICUs. Hence, this study shall focus on the morbidity, mortality, and costs associated with this infection among ICU patients. Materials and Methods: The current research is a prospective descriptive-analytical study. The study population included patients admitted to the Tertiary Referral Hospital of Kerman University of Medical Sciences who were enrolled in the study according to inclusion criteria and demographic characteristics data, length of stay in ICU and general wards, and direct and indirect medical expenses such as unemployment and rehabilitation cost, etc. Results: Nine of the 144 patients studied died. (4 in the Ventilator-Associated Pneumonia (VAP) group and 5 in the non-VAP group). Among them, the prevalence of Acinetobacter Baumannii was significantly higher than other bacteria (P-Value=0.001). The duration of hospitalization in the ICU (18±9 vs. 9.5±6 days) and recovery time (21.6±9 9.6 vs. 13.2±7 days) were higher in the VAP group (P-Value<0.05). Moreover, the duration of hospitalization in the general ward was 15.4±8 days in the VAP group and 10.6±6 days in the non-VAP group (P-Value<0.05). The cost of treatment in the VAP group ($7952.28) was significantly higher than in the non-infected group ($4400.98). The average rehabilitation cost in the VAP group was $2571.42 and in the non-affected group was $1530.88. The financial loss due to the delay in work starting was $482 in the non-VAP group which was significantly less than the VAP group ($792). Conclusion: Having VAP can significantly increase mortality, length of stay in the ICU as well as increase direct and indirect costs for patients.
Lead-tellurium oxysalts from Otto Mountain near Baker, California: I. Ottoite, Pb2TeO5, a new mineral with chains of tellurate octahedra

Abstract Ottoite, Pb2TeO5, is a new tellurate from Otto Mountain near Baker, California. Most of the mining on Otto Mountain occurred between 1940 and 1970 and is attributed to Otto Fuetterer, for whom the mountain is now named. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins, which intersect granitic rocks. Ottoite is directly associated with acanthite, bromine-rich chlorargyrite, gold, iodargyrite, khinite, wulfenite, and four other new tellurates: housleyite, markcooperite, thorneite, and timroseite. Various other secondary minerals occur in the veins, including two other new secondary tellurium minerals, paratimroseite and telluroperite. Ottoite and most other secondary minerals of the quartz veins are interpreted as having formed from the partial oxidation of primary sulfides and tellurides during or following brecciation of the veins. A later generation of quartz mineralization then recemented the breccias, effectively isolating and protecting the secondary mineralization from further alteration. Ottoite is monoclinic, space group I2/a, with the unit cell: a = 7.5353(6), b = 5.7142(5), c = 10.8981(12) Å, β = 91.330(6)°, V = 469.13(8) Å3, and Z = 4. The mineral occurs as complex spear-shaped crystals in subparallel to divergent intergrowths. It is yellow and transparent to translucent, with a pale yellow streak and adamantine luster. Mohs hardness is estimated at 3. The mineral is brittle, with an irregular fracture and two cleavages in the [100] zone at ~90°-possibly on {010} and {001}. The calculated density is 8.721 g/cm3. Ottoite is biaxial (-), with a large 2V, but indices of refraction are too high to be measured. The optic orientation could only partially be determined: Y ≈ a. No pleochroism was observed. Electron microprobe analyses provided the following averages: PbO 68.88 and TeO3 28.03, total 96.95 wt%; the empirical formula (based on O = 5) is Pb1.96Te6+1.01O5. The strongest powder X-ray diffraction lines are [dobs in Å (hkl) I]: 3.131 (2̅02) 64, 3.055 (013) 90, 3.015 (211) 100, 2.112 (2̅22) 29, 1.810 (006, 2̅15) 21, 1.773 (4̅11, 402) 43, 1.686 (033, 231) 20. The crystal structure (R1 = 0.020) consists of straight chains of trans-corner-sharing Te6+O6 octahedra parallel to a, which are joined by bonds to Pb atoms. The Pb atom exhibit markedly lopsided 11-coordination, typical of Pb2+ with stereoactive 6s2 lone-pair electrons. The powder X-ray diffraction pattern of ottoite is very similar to that reported for girdite. Examination of girdite type material suggests that its description was based upon data obtained from at least two and possibly three different phases, one of which may correspond to ottoite.
Fault‐generated mountain fronts in the central apennines (Central Italy): Geomorphological features and seismotectonic implications

The morphotectonic framework of the Central Apennines is given by faulted blocks bounded by normal faults, mostly trending NW-SE, NNW-SSE and NE-SW, which cut previous compressive structures. Such a structural setting is consistent with the lbcal mechanisms of the earthquakes which often occur in this area. In this paper, three lithologically different normal fault-generated mountain fronts are analysed in order to assess the relations between their geomorphic features and active tectonics. They border the Norcia depression (Sibillini Mts, Umbria), the Amatrice{ampotosto plateau (Laga Mts, Lazio) and the Fucino basin (Marsica Mts, Abruzzi). The Norcia depression is bounded by a N20"W trending normal fault to the east and by a parallel antithetic fault to the west. The main fault has a 1000 m throw and gives rise to a wide fault escarpment, characterized by: (l) sharp slope breaks due to low angle gravity faults; (2) important paleolandslides; and (3) several fault scarplets on the piedmont belt affecting Quaternary deposits. The Amatrice{ampotosto plateau is delimited by the western slope of Mt Gorzano which runs along a N20'W trending normal fault having a 1500m throw. Minor parallel faults dislocate Quaternary landforms. Large-scale massmovements also occur here. , "e The Fucino basin was struck by th-e 1915 Avezzano earthquake 0 : XI MCS) which produced extensive surface faulting along two parallel NW trending normal fault escarpments on the eastern border of the basin. There is paleoseismrc evidence including buried gravity graben in Late Glacial gravels and tectonic dip-slip striations on Holocene calcitic crusts covering bedrock normal fault planes. These data suggest that active extensional tectonics plays a major role in the slope morphogenesis of the Central Apennines and they indicate the importance of geomorphic analysis in seismic zonation of this area.
Sedimentary evidence relating to the tectonic evolution of the Lau Basin, SW Pacific, from ODP Sites 834–839 (ODP Leg 135)

Abstract Six sites were drilled during Ocean Drilling Program Leg 135 in the western Lau backarc basin in the southwest Pacific (Sites 834–839). These sites are all located in basins within a horst and graben terrain and form an approximate transect across the rifted arc basement onto crust considered to have been formed at the East Lau Spreading Centre. The sedimentary sequences recovered from these backarc sites range in age from the late Miocene to the Holocene; they consist primarily of a lower succession of volcaniclastic sediment gravity-flow deposits interbedded with hemipelagic clayey nannofossil oozes and nannofossil clays, overlain by a distinctive upper succession of hydrothermally stained hemipelagic, and locally redeposited, clayey nannofossil oozes. The volcaniclastic sediment gravity-flow deposits are predominantly massive, proximal, vitric gravels, sands and silts, that are mainly locally derived from adjacent basement ridges and intrabasin seamount volcanoes. At Site 835, which was drilled in a small extensional sub-basin in the oldest part of the Lau Basin, the upper clayey nannofossil ooze sequence is anomalously thick and rigorous sedimentological analysis shows that much of this sequence is redeposited. Thick clayey nannofossil ooze turbidite muds are identified that closely resemble the enclosing clayey nannofossil ooze hemipelagites. These thick turbidite muds are associated with mudclast conglomerates, interpreted as muddy debris-flow deposits, and a number of coherent rafted blocks of older hemipelagic sediment. These allochthonous deposits testify to several episodes of instability in the sub-basin that may be related to large-scale tectonic activity caused by the southward passage of ocean-ridge propagator tips past the latitude of the drillsite. Episodes of increased sediment deposition, due to increased frequency of turbidite emplacement, are evident at all of the Lau Basin backarc drillsites, and these correlate moderately well with the closest approach of the propagating ridge tip to each sub-basin. The research presented illustrates how turbidites, once identified, can be used to decipher complex tectonic histories, and demonstrates the importance of local tectonic controls on sediment redeposition in backarc basins.
An automatically updated S‐wave model of the upper mantle and the depth extent of azimuthal anisotropy

We present 3D2015_07Sv, an S wave model of the upper mantle based on the waveform modeling of 1,359,470 Rayleigh waves recorded since 1976. The use of approximate forward theory and modeling allows updating the model with new data on a regular basis. 3D2015_07Sv contains azimuthal anisotropy, achieves a lateral resolution of ∼600 km, and is consistent with other recent models up to degree 60 in the uppermost 200 km and degree 15 in the transition zone. Although radial anisotropy has been found to extend deeper beneath continents than beneath oceans, we find no such difference for azimuthal anisotropy, suggesting that beneath most continents, the alignment of olivine crystal is preferentially horizontal and azimuthally random at large scale. As most continents are located on slow moving plates, this supports the idea that azimuthal anisotropy aligns at large scale with the present plate motion only for plates faster than ∼4 cm yr−1.
Remediation of Contaminated Soil and Groundwater Using Humic Acid in Permeable Reactive Barrier for Pipeline Leakage

This paper presents the development of a new remediation technology of contaminated soil and groundwater using humic acid (HA) in permeable reactive barrier (PRB) for pipeline leakage. The objective of this study was to use humic acid that could be medium within a PRB to filter complex contaminated soil and groundwater containing chromium. Leakage of pollutants (such as hydrocarbon、gasoline、oil、wastewater、heavy metal et al) has a large economic and environmental impact. When a pipeline leak is large or undiscovered for a longer period of time, substantial volumes of gases and liquids can leak into the soil and groundwater, which can develop into dangerous situations involving costly remediation works. Traditional methods for remedying contaminated soil and groundwater from pipeline leakage, such as drilling and geochemical analysis, are destructive, time consuming and expensive. A PRB was determined to be the best option for remedying groundwater that has become contaminated with a wide range of organic contaminants (i.e., benzene, toluene, methylbenzene, xylene and polyaromatic hydrocarbons), heavy metals (i.e., lead and arsenic). The measurements show a significant increase of the adsorption of hexavalent chromium because of the complexion reaction between HA and Cr (VI) occurred under acidic condition. It could be concluded that HA could be used effectively on remediation of Cr (VI)-contaminated soil and groundwater in a wide range of pH, with or without sunlight.
Gravity anomalies of 2-D bodies with variable density contrast

A new method is presented to compute gravity anomalies that result from 2-D bodies with variable density contrast. The cross-section of a body is approximated by a polygon. Density is assumed to vary as any order of polynomial function with depth and lateral position. Results calculated by the proposed method for models with variable density contrast compare well with other methods. Liaohe basin, northeast China, is modeled from field gravity anomalies using the formulas given, showing the method is valid and effective.
Practical Server Privacy with Secure Coprocessors ∗

What does it take to implement a server that provides access to records in a large database, in a way that ensures that this access is completely private—even to the operator of this server? In this paper, we abstract this problem to a real world computer security application, and examine the question: using current commercially available technology, is it practical to build such a server, for real databases of realistic size, that offers reasonable performance—scaling well, parallelizing well, working with the current client infrastructure, and enabling server operators of otherwise unknown credibility to prove their service has these privacy properties? We consider this problem in the light of commercially available secure coprocessors—whose internal memory is still much, much smaller than the typical database size—and construct an algorithm that both provides asymptotically optimal performance, and also promises reasonable performance in real implementations. Preliminary prototypes support this analysis (but leave many areas for further work).
Stomatal Density and Ion Leakage as Indicators of Cold Hardiness in Walnut

In this work, leaf samples of one-year-old walnut cultivars and elite genotypes including 'Serr', 'Lara', 'Pedro', 'Hartley', 'Z 30 ', 'Z 63 ', 'Z 67 ' and 'Z 53 ' were taken and exposed to cold temperature at the rate of drop of 4°C per h at 0, -4, -8, -12 and -16°C. The lethal freezing temperature (LT 50 ) of cultivars and genotypes was evaluated by electrolyte leakage studies and the cultivars/genotypes were grouped into hardy, semi-hardy and non-hardy using this method. The density of stomata in the leaves of cultivars and elite genotypes rated as hardy were significantly lower than those rated as semi-hardy and non-hardy. Stomatal density of the cultivars and genotypes in the intermediate class fell within the range of hardy and non-hardy cultivars and genotypes. According to these results, number of stomata could be considered as a simple and effective anatomical selection marker for screening walnut plants for cold hardiness.
High‐latitude ionospheric electric field variability and electric potential derived from DE‐2 plasma drift measurements: Dependence on IMF and dipole tilt

[1] In this study the characteristics of electric field variability are investigated by using the sample standard deviations estimated from plasma drift measurements obtained during the Dynamics Explorer 2 (DE-2) mission. The spatial distribution of the standard deviation over the area poleward of 45° magnetic latitude and its climatological behavior with respect to the magnitude and orientation of the interplanetary magnetic field (IMF) and the dipole tilt angle (season) are examined. In comparison with past studies based on ground-based measurements and with results from a data assimilation model, this study quantifies the electric field variability with more complete spatial coverage and with more extensive climatological information and therefore is of importance to the problem of the global Joule heating estimation in thermospheric general circulation modeling. In general, the magnitude of the standard deviation exceeds the strength of the mean electric field in most of the polar area, especially under northward IMF conditions. In contrast to the climatological electric field, whose magnitude tends to be most intense in the polar cap, the standard deviation generally intensifies in the vicinity of the convection reversal and the cusp. Under most IMF clock angles the area of the largest electric field variability lies near the cusp; under the southward BZ condition the area extends toward the potential maximum on the dawn side and toward the region of strong sunward convection in the afternoon, while under the positive BY condition the area extends poleward of the potential maximum on the dawn side. The analysis reveals that electric field variability varies with magnetic latitude, magnetic local time, IMF, and season in a manner distinct from that of the climatological electric field. This indicates that empirical models and data assimilation models designed to reproduce the average electric potential or the average electric fields correctly are not necessarily well-suited to represent the squared electric fields or the electric field variability correctly.
3D Reconstruction methods based on the rational function model

The rational function model (RFM) is an alternative sensor model allowing users to perform photogrammetric processing. The RFM has been used as a replacement sensor model in some commercial photogrammetric systems due to its capability of maintaining the accuracy of the physical sensor models and its generic characteristic of supporting sensor-independent photogrammetric processing. With RFM parameters provided, end users are able to perform photogrammetric processing including ortho-rectification, 3D reconstruction, and DEM generation with an absence of the physical sensor model. In this research, we investigate two methods for RFM-based 3D reconstruction, the inverse RFM method and the forward RFM method. Detailed derivations of the algorithmic procedure are described. The emphasis is placed on the comparison of these two reconstruction methods. Experimental results show that the forward RFM can achieve a better reconstruction accuracy. Finally, real Ikonos stereo pairs were employed to verify the applicability and the performance of the reconstruction method.