Miracle-dz/UniFAR-FTUs huggingface dataset:
Extinction debt of a common shrub in a fragmented landscape

Summary 1. Environmental stochasticity and low demographic rates may cause delayed extinctions of habitat-specialist species that were initially retained within remnant patches after habitat loss and fragmentation. Detecting such extinction debts opens opportunities to counteract future biodiversity loss, yet knowing the underlying causes of population declines is a basic need for targeting specific guidelines for conservation and restoration (e.g. habitat quantity, quality or connectivity). 2. Here, we examine the extinction debt in the common Mediterranean shrub Myrtus communis (myrtle) occurring in woodland patches of a highly fragmented region that has lost nearly half of the remnant woodland cover during the last 50 years (1956–2002). 3. We sampled myrtle occurrence in 304 woodland patches and modelled its probability of occurrence in relation to patch size, patch disturbance and woodland cover in the surrounding landscape. In order to test for extinction debt evidence, we tested whether myrtle occurrence is better predicted by past (1956) than by present (2002) woodland cover. 4. We found that the probability of myrtle occurrence is associated with present patch features (size and disturbance) that are linked to causes of individual mortality and/or recruitment collapse. However, it was associated with past – rather than present – woodland cover in the surrounding landscape, proving a still unpaid extinction debt. Specifically, myrtle occurrence is very unlikely in small and highly disturbed patches located in long-term deforested landscapes. 5. Synthesis and applications. Individual longevity of the Mediterranean shrub Myrtus communis (myrtle) can delay local extinctions, but paying the debt is a matter of time, especially considering the elevated susceptibility of small and disturbed populations to environmental stochasticity. However, these populations still offer management opportunities, and reducing disturbances and improving habitat quality, especially within small woodland patches, should be a top priority for conservation and restoration.
How Valuable is Degraded Habitat to Forest Birds? A Case Study in Bachok, Kelantan

Conservationists usually pay less attention to degraded habitats than primary forests since the former areas generally support less number of species. In this study, diversity and abundance of birds inhabiting degraded habitats were recorded in order to assess the capability of these habitats in conserving birds, particularly forest species. For this purpose, five visits were done to the district of Bachok, Kelantan, Malaysia, from June 2008 until May 2009. The study area comprised mainly of small villages intersperse with small trees or shrubs and cash crop areas. A direct observation method was used to record the bird diversity in the study area. A total of 70 bird species were recorded in the study area and most of them are residents and insectivores, indicating that insects are abundant in the study area. In term of habitat utilisation, most recorded species are usually associated with open and country habitats, mangroves, as well as garden and parks. A total of nine species or 13% of the birds recorded in this area have greater association with forest habitats. Some of these forest birds were observed feeding while others having their nests in the area. Although degraded habitat in Bachok area can play important roles in conserving forest birds, the value of these habitats cannot be established since these birds are not exclusively forest dependent and can be commonly found in secondary or disturbed forests. Therefore, further studies on the behavioural aspects of forest birds need to be carried out to determine the level of resources required by forest specialists in degraded habitat.
Impaired Adipose Tissue Development in Mice With Inactivation of Placental Growth Factor Function

Placental growth factor (PlGF)-deficient (PlGF−/−) and wild-type mice were kept on a standard-fat or high-fat diet for 15 weeks. With the standard-fat diet, the body weights of PlGF−/− and wild-type mice were comparable, whereas the combined weight of subcutaneous and gonadal adipose tissues was lower in PlGF−/− mice (P = 0.02). With the high-fat diet, PlGF−/− mice had a lower body weight (P < 0.05) and less total subcutaneous plus gonadal adipose tissue (P < 0.0001). Blood vessel size was lower in gonadal adipose tissue of PlGF−/− mice with both the standard-fat and high-fat diet (P < 0.05). Blood vessel density, normalized to adipocyte number, was significantly lower in subcutaneous adipose tissue of PlGF−/− mice fed the high-fat diet (P < 0.01). De novo adipose tissue development in nude mice injected with 3T3-F442A preadipocytes was reduced (P < 0.005) by administration of a PlGF-neutralizing antibody. Bone marrow transplantation from wild-type or PlGF−/− mice to wild-type or PlGF−/− recipient mice revealed significantly lower blood vessel density in PlGF−/− recipient mice without an effect on adipose tissue growth. Thus, in murine models of diet-induced obesity, inactivation of PlGF impairs adipose tissue development, at least in part as a result of reduced angiogenesis.
Atividade reprodutiva de Physalaemus signifer (Anura, Leptodactylidae) em ambiente temporário

The breeding activity of Physalaemus signifer (Girard, 1853) was monitored from July 1999 to July 2000 in a temporary pond in Palmital, Municipality of Saquarema, State of Rio de Janeiro, Atlantic Rain Forest, Brazil. Males were sexually actives only in four nights, arriving at the pond on the early rainy season. Males in amplexus were larger and spent more nights in the reproductive aggregation than solitary ones. The number of nights was correlated with the mass of the males. Males adopted satellite behavior as alternative tactic for mate acquisition. Changes between calling and satellite tactics were observed in different nights. Calling males were not larger and heavier than satellite ones. Satellite behavior seemed to be related with the order of arrival on the pond. Size and mass of males did not influence the results of fights. Resident males won the majority of agonistics combats. Three types of vocalizations are described: advertisement, territorial, and encounter calls.
OCCURRENCE OF A EUROPEAN RED ALGA (SCHOTTERA NICAEENSIS) IN SOUTHERN AUSTRALIAN WATERS 1

Schottera nicaeensis (Phyllophoraceae, Gigartinales), presently known only from the western Mediterranean Sea and the northeastern Atlantic coasts of Europe, is reported for the first time from the Melbourne region of Port Phillip Bay in southeastern Australia. The species is perennial in the Bay, although tetrasporophytes and cystocarpic plants are commonest in late spring and early summer. This seasonal pattern, and the vegetative habits of plants during the whole of the year, show similarities to populations described by other workers for Northern Hemisphere localities where comparable water temperature and daylength regimes obtain. The small Australian S. nicaeensis community is found at 5–9 m depths and is concentrated on lighthouse foundations adjacent to the main Port of Melbourne shipping channel. It is hypothesized that the species has recently been introduced into Port Phillip Bay, and a scenario for its possible means of import on ships is suggested.
Effect of ultrasound-guided quadratus lumborum block on efficacy of postoperative analgesia after caesarean section

Objective To evaluate the effect of ultrasound-guided quadratus lumborum block (QLB) on the efficacy of postoperative analgesia after caesarean section. Methods Sixty American Society of Anesthesiologists physical status Ⅰ or Ⅱ parturients, aged 20-39 yr, weighing 50-80 kg, scheduled for elective cesarean section under subarachnoid block, were divided into 2 groups (n=30 each) using a random number table: QLB group (group Q) and control group (group C). Ultrasound-guided bilateral QLBs were performed at the end of surgery, the solution was injected into the compartment between quadratus muscle and psoas major muscles, and 0.25% ropivacaine 1.25 mg/kg was injected to each side in group Q. The parturients in both groups received patient-controlled intravenous analgesia after surgery to maintain the visual analog scale score ≤ 3, and dezocine 5 mg was intramuscularly injected as a rescue analgesic when the visual analog scale score≥4.Bruggrmann comfort scale (BCS) and Ramsay sedation scores were evaluated at 2, 4, 6, 12, 24 and 48 h after operation.The consumption of sufentanil during patient-controlled intravenous analgesia, requirement for rescue analgesia, satisfaction score of analgesia, the number of successfully delivered doses (D1) and the number of attempts (D2) were recorded within 24 h after surgery.D1/D2 was calculated.The development of respiratory depression and over-sedation was recorded.The development of QLB-related adverse reactions and postoperative nausea, vomiting, chest tightness and pruritus was also recorded. Results Compared with group C, BCS scores were significantly increased, the consumption of sufentanil was reduced, D1/D2 was increased, the requirement for rescue analgesia was decreased, and the satisfaction score of analgesia was increased (P 0.05). Adverse reactions such as respiratory depression, over-sedation, nausea, vomiting, chest tightness and pruritus were not found in two groups.Adverse reactions such as hematoma and infection at the puncture site or local anesthetic intoxication were not observed after surgery in group Q. Conclusion Ultrasound-guided QLB can enhance the efficacy of postoperative analgesia after caesarean section, reduce postoperative consumption of opioids and raise the comfort degree for parturients. Key words: Ultrasonography; Psoas muscles; Neuromuscular blockade; Cesarean section; Analgesia, patient-controlled
Phylogenetics of Echinodorus (Alismataceae) based on morphological data

Echinodorus (Alismataceae) is a genus of aquatic and semi-aquatic herbs naturally distributed from Argentina to the USA but commonly used as ornamentals in aquaria worldwide. The phylogeny of the genus was studied on the basis of 96 morphological characters. The analysis resulted in a single most-parsimonious tree supporting a polyphyletic origin of the genus. However, subgenus Echinodorus together with Echinodorus nymphaeifolius formed a clade. Two large clades can be recognized in Echinodorus s.s. , but previous subdivisions of the genus are not supported and some earlier proposed subspecific combinations were shown to be non-monophyletic. Addition of continuous characters coded as value ranges enhanced both the resolution and the support values of the tree. Hence, inclusion of continuous overlapping data is encouraged in phylogenetic studies. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 291‐305.
SPREAD OF COLLETOTRICHUM COCCODES FROM INFECTED POTATO SEED TUBERS AND EFFECT OF FUNGICIDES ON STEM INFECTION

Jason Timothy Ingram M.S. Washington State University December 2008 Chair: Dennis A. Johnson Colletotrichum coccodes, the cause of potato black dot is one of several seedborne pathogens. The quality of seed-tubers would likely improve if the interactions between seedborne inoculum and the crop were better understood. The rate of spread of C. coccodes from the seed-tuber was quantified on roots and stolons of ‘Russet Burbank’ plants grown in the greenhouse. The effect of seedborne inoculum of C. coccodes on final disease severity and potato yields was assessed in the field, and specific fungicides were evaluated for disease management. Expansion of C. coccodes foci along roots in two trials resulted in a linear growth model of 1 mm/day (P < 0.01, R 2 = 0.83). Colonization always radiated from the seed-tuber to form compact foci of infected tissue. In the field, severity of host plant colonization in belowground stems was related to percentage of infected tubers in seed lots in two of four fields (P < 0.05). Yields were not related to percentage of seed-tubers infected with C. coccodes (P > 0.1). Black dot was not a yield limiting factor under the conditions of this study, but differences in yield among seed lots (P < 0.05) from other factors illustrated the importance of selecting the
Physicochemical Properties and Starch Digestibility of Autoclaved-Cooled Water Yam (Dioscorea alata L.) Flour

Water yam (Dioscorea alata L.) is suitable for resistant starch high flour because of its high amylose content. The purple, yellow, and white water yams were treated by autoclaving and cooling with one, two, and three cycles to obtain resistant starch. Water yam tubers were cooked in an autoclave for 15 min, and then cooled prior to drying. Autoclaving–cooling of water yams decreased protein, fat, dietary fiber, water soluble polysaccharide, dioscorin, and diosgenin but increased amylose and sugar. The treatments significantly raised resistant starch and reduced in vitro starch digestibility that depended on water yam types, and affected starch granule morphology.
Effect of Weed Management Strategy and Planting Date on Herbicide Use in Peanuts (Arachis hypogaea)

Experiments were conducted in 1987 and 1988 at two locations each year to determine how two weed management strategies and three planting dates affected the cost and amount of herbicide needed to control weeds in peanuts. Weed management strategies used for each planting date included preventive, which duplicated a standard grower program, or an integrated weed management system. The least expensive strategy depended upon weed species composition, weed populations and planting date. In all cases, the integrated weed management strategy required less herbicide (acid equivalent or active ingredient) than the preventive strategy.
Concurrent Effects of Fire Regime, Grazing and Bison Wallowing on Tallgrass Prairie Vegetation

Abstract We examined the effects of fire regime and bison activity on the plant communities of active bison wallows and the surrounding grazing lawns at Konza Prairie Biological Station in northeastern Kansas, USA. In both mid-June and late July the grazed sites had higher species richness and more vegetation cover than the wallow edges regardless of fire regime. The percent cover of most dominant perennial species was significantly higher on grazing lawns than in wallows. Annual species and exotic species had significantly higher cover in wallows than in grazing lawns and in annually burned sites compared to those burned at a 4-y interval. Overall, treatment effects on community structure and individual species abundance were stronger in the June. However, in July there was significantly more bare ground wallows around sites burned at a 4-y interval, suggesting increased wallowing activity at these sites. This finding suggests a strong effect of fire regime on seasonal bison activity, which further indicates the importance of multiple interacting disturbances for generating local- and landscape-level vegetation patterns in tall grass prairie.
Systematic screening of targeted chemical combinations for cancer therapy

1410 Clinical experience and theoretical analyses suggest that multi-target approaches are required to overcome redundant and adaptive oncogenic mechanisms, and cotherapies are indeed the standard of care for many cancers. Identification of optimal and selective combinations of the many targeted agents becoming available presents a critical challenge. CombinatoRx has developed a platform for combination high throughput screening (cHTS) that we have deployed to screen combinations of approved drugs for the discovery of therapeutically relevant synergies in cell-based models. In addition to providing effective treatments, chemical synergies can provide information on interactions between targeted pathways, elucidating previously unappreciated connections between disease mechanisms. Here we extend systematic combination screening to probe perturbations of diverse cellular mechanisms to discover novel pathway interactions with therapeutic potential, and to evaluate the utility of combination-effect measures for predicting mechanisms of action for novel compounds. A set of 180 chemical probes were selected that modulate molecular targets involved in diverse cellular functions. All 16,110 pair-wise combinations of these probes were tested at multiple concentrations and ratios using cHTS in a proliferation assay with HCT116 human colon cancer cells. Interesting combinations were further evaluated for tumor selectivity using additional cell lines. The screen identified both previously reported and novel synergies and antagonisms that reflect connections between pathways relevant to cancer proliferation. Synergy profiles of compounds with proximal targets were found to be correlated, suggesting that such profiles may be used to infer mechanism of action. Combination screening data using cell lines analyzed in the context of emerging knowledge of cancer genotypes and expression profiles may lead to the development of more selective, personalized, and effective cancer therapies.
Overproduction of a mosquitocidal chloramphenicol-resistant Lysinibacillus sphaericus mutant obtained through UV irradiation

Abstract A highly active mosquitocidal mutant UV-chloramphenicol-resistant mutant (UCR-146) of Lysinibacillus sphaericus 2362 was isolated by UV irradiation and selected through resistance to chloramphenicol which was inhibitory for growth of the parent strain. The growth of UCR-146 in NYSMCL at different concentrations of chloramphenicol (20–100 µg/ml) showed high mosquitocidal activity against Culex pipiens larvae with the optimum concentration of 35µg/ml. At this level, LC50 of UCR-146 was decreased about five times from that of L. sphaericus 2362. Comparative efficiency of mosquitocidal activity of UCR-146 and L. sphaericus 2362 within 28 days of consecutive growth exhibited notable stability of both cultures through seven cycles of growth in their optimal media. UCR-146 was grown in industrial by-products media for production of the binary toxin under economic conditions. Offal medium at 2% showed the highest mosquitocidal activity of UCR-146 with LC50 of 0.53 PPM which was 16.6, 13, 12.3 and 3.4 times less than that produced with L. sphaericus 2362 grown in NYSM, L. sphaericus 2362 grown in offal, UCR-146 grown in NYSM and UCR-146 grown in NYSMCL, respectively. Hence, the mosquitocidal activity of L. sphaericus 2362 increased several times through ultraviolet (UV) irradiation followed by chloramphenicol resistance selection and then growth in 2% offal medium. Finally, this procedure for selecting UV-chloramphenicol-resistant mutant and the medium used could potentially be a simple and cost effective approach for obtaining and producing a highly active mosquitocidal mutant.
A Multilocus Molecular Phylogeny for Chaetostoma Clade Genera and Species with a Review of Chaetostoma (Siluriformes: Loricariidae) from the Central Andes

The rubbernose-pleco genus Chaetostoma comprises 47 currently valid and many undescribed species distributed along Atlantic and Pacific slopes of the Andes Mountains from Panama to southern Peru, the Coastal Mountains of Venezuela, and drainages of the Guiana and Brazilian shields. We present a five-locus molecular phylogeny for 21 described and six undescribed species of Chaetostoma spanning the geographic range of the genus. Bayesian and maximum likelihood analyses found Chaetostoma to be well supported as monophyletic and sister to a clade of central and northern Andean genera that have also been hypothesized to be closely related based on morphology (i.e., Andeancistrus, Cordylancistrus, Dolichancistrus, Leptoancistrus, and Transancistrus). Species of Chaetostoma were divided into a trichotomy consisting of: a Pacific Coast, Central American, Magdalena Basin, Lake Valencia, and Guiana Shield clade; a western Orinoco, Lake Maracaibo, and Lake Valencia clade; and a widespread upper Amazon/Orinoco clade inclusive of a single species on the Brazilian Shield. We also conducted a systematic review of species from the central Andes of northern Peru and Ecuador. Based on our phylogenetic results and direct examination of historical and recently collected type and non-type material, we describe two new species of Chaetostoma (C. bifurcum, from the Pacific Coast, and C. trimaculineum, from the Atlantic Slope), redescribe four species (C. breve, C. carrioni, C. dermorhynchum, and C. microps, all from the Atlantic Slope), transfer four species from Chaetostoma to Ancistrus and find two species to be junior synonyms.
Ethnobotanical investigation of wild edible and medicinal plants used by the Chiru Tribe of Manipur, India

The Chiru tribe is one of the scheduled tribe groups of Manipur, distributed in Senapati district, with unique cultural and ethnobotanical practices. The study has revealed the use of 69 wild edible plant species for traditional medicine and other ethnobotanical purposes by them. These reported plant species will form the basis of bioprospecting the edible medicinal plants used by the tribe. Study reveals 69 plant species belonging to 62 genera and 36 families. Most of the plant species are used in common diseases like cough, cold, diarrhoea, dysentery, diabetes, jaundice etc. and mostly consume as decoction. Such type of ethnobotanical knowledge is needed to conserve for further research and also to help the economic upgradation of the tribe.
Identification of Plasmodium Falciparum proteins interacting with the erythrocyte membrane skeleton protein spectrin

Malaria, which is caused by Plasmodium parasites, is responsible for the death of millions of humans every year in the tropical and subtropical regions of the world. Specifically P. falciparum, one of four malaria species infecting humans, is responsible for the greatest morbidity and mortality burden in African populations. The Anopheles mosquito transmits the parasite to the human host, where it infects and destroys human erythrocytes. The erythrocyte membrane therefore plays a vital role in all aspects of the pathogenic phase of the P. falciparum life cycle and protein-protein interactions between host and parasite are thus a key focus of research. The human erythrocyte maintains its shape with a structural network of proteins underneath the plasma membrane and the main protein component of this erythrocyte membrane skeleton is spectrin. To investigate host-parasite protein interactions, a novel application of phage display technology was developed, whereby purified human erythrocyte spectrin was biopanned against a P. falciparum phage-display library. The P. falciparum DNA inserts of interacting phage were compared to the PlasmoDB database and five interacting proteins were identified: a putative aminopeptidase (PfM18AAP); a putative Ebl-1 like protein, which is proposed to participate in erythrocyte invasion; and three hypothetical proteins. The interaction of the hypothetical proteins with spectrin is the first information available on the function of these proteins. The five gene sequences were cloned into the pET-15b or pGEX-4T-2 expression vectors for purification of the recombinant proteins from Escherichia coli. Only the 6HisPfM18AAP fusion protein was expressed in soluble form and purified by affinity selection. PfM18AAP migrated as a 67 kDa peptide on SDS-PAGE and native gel analysis revealed multiple subunits of the enzyme, predominantly a tetramer and higher oligomers. Cleavage of the 6His-tag and subsequent IEF SDS-PAGE revealed three 65 kDa entities with pI ~6.6, ~6.7 and ~6.9. An in vitro coupled enzyme assay showed that PfM18AAP cleaved an N-terminal aspartate from a peptide substrate with a maximum activity at pH 7.5 and 37 oC. Inhibitor studies confirmed that the enzyme is a metalloprotease. Blot overlay assays with PfM18AAP against spectrin and erythrocyte membrane proteins verified that