Miracle-dz/UniFAR-FTUs huggingface dataset:
Speciation and adaptive radiation of subterranean mole rats, Spalax ehrenbergi superspecies, in Jordan

Abstract The major initial mechanism of speciation in subterranean blind mole rats, Spalacidae, is chromosomal, primarily through Robertsonian rearrangements. Here we highlight another scenario of chromosomal rearrangement leading to ecological speciation and adaptive radiation apparently initiated by pericentric inversions and genic divergence to different ecologies in mole rats in Jordan. We analysed karyotype, allozyme, size and ecological diversity across the range of mole rats in Jordan from mesic Irbid in the north to xeric Wadi Musa (Petra region) in the south, a transect of 250 km. We examined mole rats for chromosome ( N =71), size ( N =76), and allozyme ( N =67) diversities, encoded by 32 loci, in 12 populations of the Spalax ehrenbergi superspecies in Jordan. By a combination of chromosome morphology, genetic distance, body size and ecogeography, we identified four new putative biological species. All species (except two animals in Madaba) share 2 n =60 but vary in chromosome morphology, caused by pericentric inversions and/or centromeric shifts. The «north Moav» species is karyotypically polymorphic for 2 n (2 n =60; including locally also two animals with 2 n =62). The distribution of the four species is associated with ecogeographical different domains and climatic diversity. Genetic diversity indices were low, but like chromosome arms (NFa) were positively correlated with aridity stress. Discriminant analysis correctly classified 91% of the individuals into the four species utilizing combinatorially chromosome, allozyme and size diversities. It is hypothesized that mole rat evolution underground is intimately associated with climatic diversity stress above ground.
Associated Features with Non-Sentinel Lymph Node Involvement in Early Stage Breast Cancer Patients who Have Positive Macrometastatic Sentinel Lymph Node.

Objective The main goal of this study is to determine the clinico-pathological factors that correlate non-sentinel lymph nodes (LNs) involvement in clinically node negative breast cancer (BC) patients with positive macrometastatic sentinel lymph node (SLN) in order to derive future evidence to define a subgroup where completion axillary lymph node dissection (cALND) might not be recommended. Materials and Methods Total 289 SLN biopsies were performed in clinically node negative BC patients between March 2014 and April 2017. Seventy patients who performed cALND due to positive macrometastatic SLN were retrospectively selected and classified into two groups, according to non-SLN involvement (NSLNI). Clinico-pathological features of patients were examined computerized and documentary archives. Results Extracapsular extension (ECE) of SLN, number of harvested SLNs, metastatic rate of SLNs, absence of ductal carcinoma in situ (DCIS) and presence of multilocalization were significantly associated with the likelihood of non-SLN involvement after univariate analysis (p<0,05). Absence of DCIS and presence of multilocalization were found to be significant after multivariate analysis. Conclusion Careful examination of clinico-pathological features can help to decide avoiding cALND if enough LNs are removed and the rate of SLN metastases is low, particularly in case DCIS accompanying invasive cancer in patients without multi localized tumour.
Comparative study between over underlay with classical underlay techniques of tympanoplasty

Background: The objective of the study was to compare the over underlay tympanoplasty technique with classical underlay tympanoplasty in terms of hearing impairment, graft acceptance and complications. Methods: 60 patients of chronic otitis media, mucosal, inactive, aged between 16-60 years who presented to ENT OPD with small, medium, large and subtotal perforations having mild to moderate conductive hearing loss were included in the study. After taking informed consent, patients were randomly divided into 2 groups containing 30 patients each. In group A, graft was placed medial to the handle of malleus and medial to the annulus (underlay technique), while in group B, graft was placed lateral to the handle of malleus and medial to the annulus (over underlay technique). Both groups were reviewed after 6 months. Pre-operative and post-operative air bone gap were compared. Surgery was considered successful based on post-operative graft uptake, hearing improvement and maintenance of middle ear space. Results: In group A, re-perforation was seen in 8 cases (26.7%) whereas only 3 cases (10%) in group B had re-perforation. Medialization was noted among 4 patients in group A (13.3%), and was absent in group B. Lateralization was absent in both the groups. Post-operative hearing threshold in group A was 6.2±4.56 dB and in group B was 11.45±7.38 dB. Conclusions: Over underlay tympanoplasty is a safer technique as compared to classical underlay, showing lower rates of re-perforation or medialization and a significant improvement in hearing. Hence over-underlay is an effective method, having higher success rates.
Food partitioning among Lake Malawi nearshore fishes as revealed by stable isotope analyses

Within the Great Lakes of Africa there exist the world's most diverse communities of freshwater fishes (Fryer and Iles 1972, Greenwood 1974, Ribbink et al. 1983). In particular, the nearshore waters of Lakes Malawi and Tanganyika contain flocks of species, mostly members of the family Cichlidae, which may attain densities of up to 22 species and >500 individuals in a 50-M2 area (Ribbink et al. 1983). While many of these cichlid species are very similar in general body morphology, there is high interspecific diversity in neurocranial morphology and dentition (Fryer and Iles 1972, Reinthal 1990a). This morphological diversity suggests that interspecific differences in feeding strategies may play an important role in reducing interspecific competition and maintaining high species diversity (Fryer and Iles 1972, Reinthal 1990a). Yet the results of studies investigating feeding habits of cichlids have been equivocal. Initial studies of the stomach contents of rock-dwelling fishes (Fryer 1959, Ribbink et al. 1983) showed little or no evidence of food partitioning. This, along with laboratory studies (Liem 1984), suggested that herbivorous cichlids, while being facultative specialists, are generally nondiscriminatory feeders. In reviewing the available literature on cichlid feeding habits, Greenwood (1981:71) concluded that "there is apparently complete interspecific overlap in environmental requirement. " If this is true, then partitioning may occur only during periods of low food supply (McKaye and Marsh 1983). More recent research (Van Oijen 1982, Reinthal 1990b) has found significant variation of stomach contents among cichlid species. However, because stomach contents represent food consumed over a small time period and within a small area, these results do not conclusively demonstrate whether food partitioning is the exception or the rule. Other disadvantages of stomach content analyses include difficulty of identification and uncertainty over whether all observed stomach contents are assimilated to the same degree, or if some components, such as cyanobacteria, are indigestible (Fryer 1959, Ribbink et al. 1983, Reinthal 1990b). In this note we present evidence for food resource partitioning among fishes of Lake Malawi, Africa, by comparing the stable isotope composition (b13C and b15N) of a number of nearshore fish species and their potential food sources. Because a fish's isotopic composition represents a spatio-temporal integration of the composition of assimilated food, this approach circumvents many of the problems in stomach analyses noted above.
Partitioning of locomotor and feeding metabolism in sablefish (Anoplopoma fimbria)

The swimming, feeding, and standard metabolic rates of the sablefish (Anoplopoma fimbria) were determined using tunnel and mass respirometers. Swimming metabolic rate was measured for fish in both digestive and nondigestive states. Comparison of power–performance curves for fed and starved states suggested that sablefish were able to allocate oxygen supply preferentially to locomotor muscles and suppress the oxygen demand of digestion when active. Reduced blood flow to the stomach, liver, and spleen during exercise has been observed in other species and may provide a physiological mechanism to explain the results obtained with sablefish.
Can insect data be used to infer areas of endemism? An example from the Yungas of Argentina.

El objetivo principal de este trabajo es analizar si las areas de endemismo pueden ser caracterizadas cuantitativamente utilizando insectos, los cuales generalmente se encuentran mucho mas pobremente muestreados que vertebrados y plantas. La busqueda de areas de endemismo fue realizada utilizando un criterio de optimalidad sobre aproximadamente 1,100 georreferencias de 288 especies de insectos holometabolos presentes en la region de estudio. Esta corresponde al noroeste de la Argentina, especificamente en las Yungas (un bosque lluvioso montano muy humedo). El software NDM/VNDM, que aplica dicho criterio de optimalidad, fue usado para buscar areas de endemismo (i.e. conjuntos de celdas definidos por dos o mas especies). Se utilizaron cinco tamanos de grilla: tres cuadrados (Io, 0.5° y 0.25°) y dos rectangulares (0.25° x 0.5° y 0.5° x 0.25°). Los resultados de este estudio indican que las Yungas pueden ser caracterizadas como una unidad biogeografica con identidad propia y estos resultados concuerdan con propuestas biogeograficas previas. Se obtuvieron 26 areas de endemismo con 23 especies endemicas de insectos (en 14 familias) restringidas a Yungas y 46 especies (en 10 familias) endemicas, presentes en Yungas y habitats adyacentes. Nuestro analisis sugiere que el uso de insectos puede ser una herramienta poderosa para identificar areas de endemismo, aun considerando lo fragmentario del conocimiento actual de estos grupos en America del Sur. El uso de diferentes tamanos de grilla fue crucial. Tamanos pequenos y medianos son altamente recomendados para identificar patrones diferentes. El metodo cuantitativo utilizado permitio identificar areas de endemismo dificiles de reconocer con metodos biogeograficos tradicionales, tales como areas disyuntas o parcialmente superpuestas.
Annual Growth Cycle, Growth Potential, and Growth Compensation in the Bluegill Sunfish in Northern Indiana Lakes

Eight lake populations of the bluegill sunfish (Lepomis macrochirus) with widely varying growth rates exhibited a surge of growth in the spring followed by a progressively declining growth rate in late summer and autumn. The growth rate declined as age increased; in no case did the growth of an older age group exceed that of a younger age group in the same year. Increase in length was estimated from marginal growth of scales collected at various times throughout 1962 and 1963.The beginning of the growing season, assumed to correspond in time with the formation of the annulus, was estimated to average April 8 in 1962 and April 26 in 1963. The time of annulus formation was observed in one lake by collecting scales when the mark was appearing, and in the others it was estimated by extrapolation of a regression between marginal scale growth and time. The end of the growing season, or the time when 90% of annual growth had been achieved, came on September 10 in 1962 and on September 27 in 1963. The length of t.
Cutting the carnage: wildlife usage of road culverts in north-eastern New South Wales

Culverts have been used for a number of decades in Europe and the USA to reduce wildlife road-kills. In Australia, culverts have been employed by road authorities only relatively recently. This study used sand-strip surveys to investigate wildlife usage of nine purpose-built culverts along a 1.4-km section of the Pacific Highway at Brunswick Heads, north-east New South Wales. Surveys during two eight-day periods in spring and summer 2000 found 1202 traverses by wildlife through the culverts. Frequent culvert users were bandicoots (25% of traverses), rats (25%), wallabies (13%) and cane toads (14%). All culverts were used by these species, suggesting that at least several individuals of each species were involved. Infrequent users (each <2% of crossings) were possums, echidnas, lizards, birds and introduced carnivores. A koala was recorded crossing on two occasions. The long-nosed potoroo was observed in the surrounding habitat but was not confirmed traversing the culverts. Surveys for road-kills on this road section suggest that the exclusion fence bordering the highway prevented mammal road-kills and channeled mammals to the culverts. A single survey on a wet night found many frogs crossing the road surface and many were killed. This study confirms that culverts and exclusion fencing facilitate safe passage across a road for a range of wildlife species. This suggests that this form of management response to extensive road mortality of wildlife is appropriate and should be adopted more widely. However, this form of mitigation is not effective for frogs.
Patients Infected by Extended-Spectrum Beta-Lactamase Producing Klebsiella pneumoniae: Risk Factors and Outcomes

Infections due to resistant bacteria including Extended-Spectrum Beta-Lactamase (ESBL) producing Klebsiella pneumoniae becomes the major health problem worldwide. The aim of this study is to understand the prevalence of ESBL producing K. pneumoniae in Intensive Care Unit (ICU) dr. Cipto Mangunkusumo National Hospital (CMNH) and also to understand the risk factors related to these bacteria and its correlation with patients' outcomes. This retrospective study using the sample from clinical isolates of ICU's patients in CMNH who were treated in 2011 and known to have an infection with the K. pneumoniae based on microbiological examination. Phenotypic confirmation for ESBL conducted using double disk synergy test (DDST) and patient's history of illness was traced through the medical record. From 35 patients infected by K. pneumoniae, 25 isolates were ESBL positive. Central venous catheter (CVC) utilization is found to be a probable risk factor in getting an infection by such bacteria. Infection by ESBL producing K. pneumoniae could prolong ICU stays more than 20 days. Infeksi oleh Klebsiella pneumoniae penghasil Extended-Spectrum Beta-Lactamase (ESBL): Faktor Risiko dan Luaran Klinis Infeksi yang disebabkan oleh bakteri resisten termasuk Klebsiella pneumoniae penghasil ExtendedSpectrum Beta-Lactamase (ESBL) saat ini menjadi masalah kesehatan utama di seluruh dunia. Tujuan penelitian ini adalah untuk mengetahui prevalensi K. pneumoniae penghasil ESBL di Intensive Care Unit (ICU) Rumah Sakit Umum Pusat Nasional dr. Cipto Mangunkusumo (RSUPNCM) serta mengetahui faktor risiko terkait infeksi oleh bakteri tersebut dan hubungannya dengan luaran klinis pasien. Penelitian ini merupakan suatu studi restrospektif pada isolat pasien ICU RSUPNCM yang dirawat pada tahun 2011 dan diketahui mengalami infeksi oleh bakteri K. pneumoniae berdasarkan pemeriksaan mikrobiologi. Uji konfirmasi fenotip ESBL dilakukan dengan teknik DDST dan data pasien ditelusuri pada rekam medik. Dari 35 pasien yang terinfeksi oleh K. pneumoniae, 25 isolat merupakan penghasil ESBL. Penggunaan kateter vena sentral dapat menjadi faktor risiko terinfeksi oleh K. pneumoniae penghasil ESBL dan infeksi oleh bakteri tersebut dapat memperpanjang lama rawat pasien di ICU hingga lebih dari 20 hari.
The Bryozoan Rhynchozoon larreyi (Audouin, 1826)–A Successful Competitor in Coral Reef Communities of the Red Sea

Rhynchozoon larreyi (Audouin, 1826) is a successful competitor for space in sessile reef communities at Port Sudan and Eilat (Red Sea). At these localities it has always been found in association with Zanclea sp. The relationship between the two species is regarded as mutualistic. The hydroid benefits through association with a successful spatial competitor; the bryozoan gains advantage through protection of its surface from predation and fouling. Morphological modification of the bryozoan colony in response to this association leads to a highly organized reticulate surface pattern, which provides both symbionts with access to feeding currents.
High resolution flatness measurements on diffuse and scattering surfaces

The use of interferometry for very high accuracy area mapping of the flatness of optical surfaces is a well-known, high-performance tool. However, it is difficult to make a high-performance measurement over a full area of a diffuse or scattering surface such as a machined metal or metal powder used in manufacturing. This challenge is generally addressed with scanning methods using laser lines, confocal or other point scanners of mechanical means such as coordinate measuring machines. Data collection with these method can be very slow, due in part from the flexibility to measure a large change in contour that is not critical to most flatness applications. Previously, we reported on a moire method for diffuse or powder surfaces that is not unlike the Ronchi tests using in process of ground glass. This paper discussed some of the challenges of making this type of measurement and suggests a new hybrid method that trades of the capability for providing profiles over relatively large measurement ranges for obtaining very high sensitivity to errors from the ideal flat surface
Reproduction in the short‐nosed fruit bat in relation to environmental factors

The reproductive pattern of the short-nosed fruit bat Cynopterus brachyotis in a tropical dry evergreen rainforest in Thailand (13°N) is characterized by seasonal bimodal polyoestry with postpartum oestrus. The first lactation period occurred in March–April, but the timing of the second varied between years: September–October in 1998 and July–August in 1999. Females may experience reproductive delays after the second parturition. Females attained sexual maturity at 6–7 months of age and gave birth for the first time at about 11–12 months, and are able to produce two young a year. Females born in April gave birth as early as March the following year. Those born in August–September first gave birth in July–August the following year. Males attained sexual maturity when they were a year old. Testis size was significantly positively correlated with photoperiod. The body weight of mature males varied cyclically, was higher during breeding periods and was significantly correlated with testis size. The first parturition coincided with the onset of the annual rains and the second occurred in the middle of the rainy season. Both lactation and weaning periods correspond with high food availability. A significantly higher percentage of reproductive females, earlier parturition, greater synchrony of lactation, higher body mass of lactating females, more abundant, larger and heavier juveniles, and heavier mature males were recorded in 1999 compared with 1998. The El Nino Southern Oscillation resulted in a prolonged and severe drought early in 1998, and induced mast fruiting in 1999 that led to higher reproductive success. Photoperiod may regulate the reproductive rhythm in male C. brachyotis, although experimental studies are required to verify this.
Population responses of the Endangered White-breasted Thrasher Ramphocinclus brachyurus to a tourist development in Saint Lucia – conservation implications from a spatial modelling approach

Summary Tourism development is one of the main contemporary drivers of habitat loss and fragmentation within the Caribbean Islands biodiversity hotspot. In Saint Lucia, construction of a hotel and golf course within coastal dry forest is directly threatening the largest known subpopulation of the Endangered White-breasted Thrasher Ramphocinclus brachyurus. Understanding how the species is responding to ongoing landscape change and identifying priority sites for conservation are imperative for planning its long-term conservation. In this study, a four year White-breasted Thrasher monitoring dataset (2006–2009) and landscape-scale environmental variables were used to: a) identify, characterise and map spatio-temporal patterns of White-breasted Thrasher encounter rate (an abundance proxy) within and outside the tourist development site; b) determine landscape-scale environmental variables that influence such patterns, and c) produce an island-wide predictive map of potentially suitable habitat. Observed patterns in encounter rates within and outside the development site were consistent with thrashers being displaced from cleared areas of forest and crowding into intact forest patches to the north and west of the golf course. A year after the period of the most extensive habitat clearance, White-breasted Thrasher numbers declined markedly leading to a 55% reduction in encounter rate within the development site over the four years of the study. The habitat suitability model predicted that a range of sites outside of the known geographic range of the thrasher are potentially suitable, some of which merit further surveys for potentially undetected populations. Given these findings, it is vital that patches of suitable dry forest adjacent to the tourist development are protected and contiguous natural habitat inside the tourist development is preserved.
Vertical distribution and diurnal migration patterns of Jasus edwardsii phyllosomas off the east coast of the North Island, New Zealand

Abstract The rock lobster Jasus edwardsii forms the basis of important fisheries in south‐eastern Australia and New Zealand. Their long pelagic larval phyllosoma phase (12–24 months) raises many questions as to how the larvae are retained and/or recruited into local populations. Recent attempts to model the dispersal of J. edwardsii phyllosoma have had mixed success at reconstructing settlement patterns. However, these models have either ignored vertical distribution or have used that of the western rock lobster, Panulirus cygnus. We report on the vertical distribution and migration of J. edwardsii phyllosomas, collected in March/April 2003 from the Wairarapa Eddy off the east coast of the North Island, New Zealand, and provide a model to describe their vertical distribution. J. edwardsii phyllosoma were primarily recorded within the upper 100 m over similar depth ranges to those reported for other palinurid and scyllarid species. Well‐defined changes in diel vertical distribution were restricted to late‐stage larvae. Mid‐stage phyllosomas were concentrated in the upper 20 m both day and night. Late‐stage phyllosomas were concentrated in the upper 20 m during the night, but they were absent from the upper 20 m during the day and distributed primarily between 20 and 100 m. Future modelling will benefit from using larval distribution and behaviour patterns specific to J. edwardsii.