Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring the ancestry of parents and grandparents from genetic data

Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixture tract lengths in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of decomposition of an individual’s admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. We perform extensive simulations to quantify the error in the estimation of ancestral admixture proportions under various conditions. To illustrate the utility of the method, we apply it to real genetic data. Author summary Ancestry inference is an important problem in genetics and is used commercially by a number of companies affecting millions of consumers of genetic ancestry tests. In this paper, we show that it is possible, not only to estimate the ancestry fractions of an individual, but also, with some uncertainty, to estimate the ancestry fractions of an individual’s ancestors. For example, if an individual traces his/her ancestry 50% to Asia and 50% to Europe, it is possible to distinguish between the individual having two parents that each are 50:50 composites of Asian and European ancestry, or one parent from Asia and one from Europe. It is likewise also possible to make inferences about grandparents. We present a computationally efficient method for making such inferences called PedMix. PedMix is based on a probabilistic model for the descendant and the recent ancestors. PedMix infers admixture proportions of recent ancestors (parents, grandparents or even great grandparents) using whole-genome genetic variation data from a focal individual. Results on both simulated and real data show that PedMix performs reasonably well in most scenarios.
Isolation, identification and technological properties of lactic acid bacteria from raw cow milk

Lactic acid bacteria are used as starter culture for the production of fermented dairy products, and that occur naturally as indigenous microbiota of the raw milk. In this study, lactic acid bacteria were isolated from raw cow milk samples. The serial dilutions of raw milk were made and plated onto LM17 agar and MRS agar adjusted to pH 5.4. The isolates were firstly identified based on cell morphology, reaction to gram stain, catalase production, growth in MRS broth containing 2%, 4%, and 6.5% NaCl, growth ability of different temperatures and formation of gas in MRS broth. Acid formation in 10% reconstituted skim milk and antimicrobial activity against foodborne pathogens Listeria monocytogenes ATCC 7644, Stapylococcus aureus ATCC 25923, and Clostridium perfringens ATCC 13124 were examined using agar well diffusion method. The total of 90 LAB isolates were classified as Lactobacillus (37.78%), Lactococcus (36.67%), Enterococcus (20.00%), Streptococcus (4.44%), and Leuconostoc (1.11%). Based on technological properties, 56 of 90 isolates (42 cocci, 14 rods) were selected, and further identified at the species level using API 20 Strep and API 50 CH identification system, respectively. The Lactobacillus isolates were identified as Lactobacillus acidophilus, Lactobacillus fermentum, Lactobacillus paracasei ssp. paracasei, Lactobacillus plantarum, Lactobacillus delbrueckii ssp. lactis, and Lactobacillus rhamnosus. The enzymatic profiles of the 17 selected isolates were studied with API ZYM system. The Lactobacillus spp. strains tested displayed high leucine arylamidase activity. Two Lactococcus lactis ssp. lactis AKS320.1 and AKS320.2 strains and one Enterococcus faecalis AKS424 strain were able to produce bacteriocin. In conclusion, some of these isolates could be considered as potential starter culture candidates for fermented milk products.
Market, Policies and Local Governance as Drivers of Environmental Public Benefits: The Case of the Localised Processed Tomato in Northern Italy

This article explores the role of a specific Localised Agri-food System (LAFS) in the provision of Environmental and social benefits (ESBs) in densely cultivated, industrialised, and populated areas by analysing the core of the processing tomato supply chain of northern Italy (Parma and Piacenza). The research examines how the interplay of market drivers, public policies, and collective actions favoured farming, technological, and organisational innovations geared to support long-term economic growth and tackle, at the same time, environmental challenges. The tomato supply chain is characterised by a favourable convergence of attitudes, policies, and market conditions that over time allowed for fruitful interactions between private stakeholders and between the supply chain and public players. Decades of key stakeholders’ interconnections within the tomato supply chain led to a success story of economic growth and attention to a new balance between agro-industry and environment, for the benefit of producers/processors, consumers, and natural resources. Profitability strategies inevitably imply intensification of farming in order to maximise profit levels per hectare, however, the tomato supply chain found a collective motivation that could grant profitability and concurrently reward producers and processors for attention paid to safeguarding the environment—giving evidence that intensification does not necessarily conflict with requirements in support of sustainability.
Household Transmission Study of Cryptosporidiosis in Bangladesh

Background Cryptosporidium, an apicomplexan protozoa, is a leading contributor to diarrheal morbidity and mortality in children under five years old worldwide. As there is no vaccine and no approved drug for Cryptosporidium spp. in young children, preventing parasite transmission is crucial. We undertook a pilot case-control study to define the extent of person-to-person transmission of cryptosporidiosis within families in an urban and rural community in Bangladesh. Methods We enrolled 48 case families with a Cryptosporidium-infected child aged 6-18 months. Controls were age-sex matched Cryptosporidium-negative children (n=12). Once children were identified, we enrolled all household members. We then followed these individuals for 8 weeks, with weekly surveillance stools and testing with qPCR for Cryptosporidium spp. Findings In the 48 case families, the rate of secondary infections with Cryptosporidium was 18.6% (22/118) compared to 0 new infections (0/35) in the 12 control families. In the 22 urban Mirpur households, the secondary attack rate was 30% (18/60) in cases compared to 0% (0/14) in controls (chi-square p = 0.018). In contrast, in the 21 rural Mirzapur households, the secondary attack rate was 6.9% (4/58) in case households compared to 0% (0/21) in controls (chi-square p = 0.22). Genotyping by gp60 demonstrated infection with the same subspecies in five of six families. Serologic response to Cryptosporidium infection was associated with younger age, longer duration of infection, and C hominis gp60_IbA9G3R2 infection. Interpretation The high rate of secondary infection in Mirpur suggests that person-to-person transmission is likely a major source of Cryptosporidium infection for young children living in this region. GP 60 genotyping demonstrated direction of infection in 2 households, and concurrent infection in five households. Further work is needed to understand the differences in parasite transmissibility and immunity to different genotypes.
Occurrence of Fin Whales (Balaenoptera physalus) Between Vancouver Island and Continental North America

Abstract Historically, Fin Whales (Balaenoptera physalus) were relatively common off the west coast of North America but very few records of their occurrence in waters between Vancouver Island and continental North America exist. To confirm their presence in these waters we collected photographs documenting at least 13 unique individuals during 43 encounters from 1999 to 2017. These records are the first of live Fin Whales in Queen Charlotte, Johnstone, Georgia and Juan De Fuca Straits and are also the only confirmed sightings between Vancouver Island and continental North America since 1930. Additionally, 12 dead Fin Whales all with evidence of ship strikes are reported in these waters between 1986 and 2017. Most (88%) sightings of live Fin Whales occurred between July and October and no individuals were documented dead or alive between January and April. We suggest that Fin Whales in coastal waterways may be at greater risk to ship strikes and predation by mammal-eating Killer Whales (Orcinus orca) than in less confined waters further offshore.
Attractive males produce high‐quality daughters in the bean bug Riptortus pedestris

There are numerous studies on the genetic benefit of female mate choice. Fisherian benefits are detected frequently, in which attractive males benefit females by increasing the mating success of sons. In contrast, good‐genes benefits are relatively small or undetectable, especially as males often face a trade‐off between the expression of secondary sexual traits and viability. In this situation, the effects of good genes might be masked in their sons and, therefore, should be investigated in daughters. A previous study has shown that attractive males produce attractive sons (i.e., Fisherian benefit); the present study aimed to verify the existence of good‐genes benefits by revealing whether attractive males of the bean bug Riptortus pedestris (Fabricius) (Hemiptera: Alydidae) produced high‐quality daughters. Male attractiveness was measured using courtship latency, and the fitness of the females and their offspring was measured based on their lifetime reproductive success as well as the longevity of the daughters. There was no evidence that females directly benefited from mating with attractive males. Whereas male attractiveness (i.e., courtship latency) did not affect nymphal viability or the longevity of daughters, the attractive males with lower courtship latency could produce the daughters with higher lifetime reproductive success. These results suggest that female mating preference in R. pedestris evolved via Fisherian and good‐genes benefits.
Anticancer Effects of LBA-ST Yogurt Supernatant on HeLa Cells via Heat Shock Protein 27 Decrease In Vitro

Heat Shock Protein 27 (Hsp27) is overexpressed in cervical cancer as a response to stress conditions. Hsp27 overexpression increase invasion, migration, and adhesion pathways of cancer cells. The Yogurt supernatant contains Short-Chain Fatty Acids (SCFA) include acetate, lactate, and butyrate which have anticancer activity. This study aimed to investigate supernatant of LBA-ST ( Lactobacillusbulgaricus-acidophilus, Streptococcusthermophillus) Yogurt can decrease the expression of Hsp27 in HeLa culture cells. The mechanism on how supernatant yogurt inhibit invasion, migration, and adhesion was studied by immunocytochemistry. The data was then collected and analyzed using One-Way ANOVA. From this study, it can be concluded that the expression of proteins that play a role in invasion, adhesion, and migration of the Hsp27 was proven to be decreased (p< 0.05 ± 0.005). Keywords: HeLa cells, yogurt supernatant, Lactobacillus bulgaricus - acidophilus, Streptococcus thermophillus , Hsp27
Identification and Characterization of Bioactive Peptides of Fermented Goat Milk as a Sources of Antioxidant as a Therapeutic Natural Product

The increasing of functional food is rising in line with public awareness for healthy food consumption. Provision of functional food source is developed through enhanced bioactive that has a regulatory function for body. Bioactive peptides in milk is known have variety of beneficial function of the body such as immunomodulator, immunostimulatory, anti-hypertension, anti-hyper cholesterol, as well as a variety of other beneficial function. The aim of this study is to obtain fermentation methods to product functional dairy product contain bioactive peptides and beneficial of fermented goat milk. The result of this study showed that goat milk fermented using 3 % commercial starter able to produce the best yoghurt than using local yoghurt starter. Analysis of protein content showed that the fermentation processing increased the amount of protein in goat milk sample. Using SDS-PAGE showed that the breakdown of protein into fraction of fermented goat milk greater than unfermented goat milk. The result of fractional protein was analyzed by LC MS/MS and showed that there were three kind bioactive sequences of bioactive peptides. Each of which consist of 16 amino acids that safely protected from gastrointestinal animal model that fed by dietary treatment of hypercholesterolemia.
Afferent information modulates spinal network activity in vitro and in preclinical animal models

Article history: Received 29 July 2016 Received in revised form 13 September 2016 Accepted 14 September 2016 Available online 15 September 2016 Tactile hypersensitivity is one of themost debilitating symptoms of neuropathic pain syndromes. Clinical studies have suggested that its presence at early postoperative stages may predict chronic (neuropathic) pain after surgery. Currently available animal models are typically associated with consistent tactile hypersensitivity and are therefore limited to distinguish betweenmechanisms that underlie tactile hypersensitivity as opposed to mechanisms that protect against it. In this study we havemodified the ratmodel of spared nerve injury, restricting the surgical lesion to a single peripheral branch of the sciatic nerve. This modification reduced the prevalence of tactile hypersensitivity from nearly 100% to approximately 50%. With this model, we here also demonstrated that the Regulator of G protein Signaling 4 (RGS4) was specifically up-regulated in the lumbar dorsal root ganglia and dorsal horn of rats developing tactile hypersensitivity. Intrathecal delivery of the RGS4 inhibitor CCG63802 was found to reverse tactile hypersensitivity for a 1 h period. Moreover, tactile hypersensitivity after modified spared nerve injury was most frequently persistent for at least four weeks and associated with higher reactivity of glial cells in the lumbar dorsal horn. Based on these datawe suggest that this new animalmodel of nerve injury represents an asset in understanding divergent neuropathic pain outcomes, so far unravelling a role of RGS4 in tactile hypersensitivity.Whether thismodel also holds promise in the study of the transition from acute to chronic pain will have to be seen in future investigations. © 2016 Published by Elsevier Inc.
Lysyl oxidase inhibition drives the transdifferentiation from lung adenocarcinoma to squamous cell carcinoma in mice

LKB1 is frequently mutated in human non-small cell lung cancer (NSCLC) and Lkb1 deletion in mice triggered the lung adenocarcinoma (ADC) to squamous cell carcinoma (SCC) transdifferentiation (AST) through lysyl oxidase (LOX)-dependent extracellular matrix remodeling. Here we show that pharmacological inhibition of lysyl oxidase in KrasG12D/Trp53L/L mouse model, which is known to produce lung ADC only, triggers the ADC-to-SCC transdifferentiation independent of LKB1 status. Treatments of two different inhibitors of lysyl oxidase decrease collagen deposition and promote redox accumulation, and eventually trigger the AST. Importantly, these transited SCC show strong resistance to lysyl oxidase inhibition in stark contrast to ADC. Collectively, these findings establish a new AST mouse model independent of LKB1 inactivation status.
Vibrational imaging based on stimulated Raman scattering microscopy

A stimulated Raman scattering microscope with near-infrared picosecond laser pulses at high repetition rates (76 MHz) and radio-frequency lock-in detection is accomplished. Based on stimulated Raman loss detection, we demonstrate noninvasive point-by-point vibrational mapping of chemical and biological samples with high sensitivity and without the requirement for labeling of the sample with natural or artificial fluorophores. We experimentally demonstrate a major benefit of this technique, which is the capability to respond exclusively to the linear Raman-resonance properties of the sample, thus allowing a direct quantitative interpretation of image contrast in terms of the number density of Raman-active modes.
Biological responses of Crested and Least auklets to volcanic destruction of nesting habitat in the Aleutian Islands, Alaska

ABSTRACT Crested Auklets (Aethia cristatella) and Least Auklets (A. pusilla) are crevice-nesting birds that breed in large mixed colonies at relatively few sites in the Aleutian Island archipelago, Bering Sea, Gulf of Alaska, and Sea of Okhotsk. Many of these colonies are located on active volcanic islands. The eruption of Kasatochi volcano, in the central Aleutians, on August 7, 2008, completely buried all crevice-nesting seabird habitat on the island. This provided an opportunity to examine the response of a large, mixed auklet colony to a major geological disturbance. Time-lapse imagery of nesting habitat indicated that both species returned to the largest pre-eruption colony site for several years, but subsequently abandoned it within 5 yr after the eruption. In 2010, a rockfall site in a cove north of the old colony site began to accumulate talus, and groups of auklets were observed using the site in 2011. Use of the new colony appeared to coincide with the abandonment of the old colony site by both species, though surface counts suggested that Least Auklets shifted to the new colony sooner than Crested Auklets. At-sea surveys of seabirds before and after the eruption indicated that both Crested and Least auklets shifted their at-sea distributions from the waters around Kasatochi Island to nearby Koniuji Island. In combination, at-sea counts and colony time-lapse imagery indicated that Crested and Least auklets using Kasatochi responded to the volcanic disturbance and complete loss of nesting habitat at the main colony on Kasatochi with dispersal either to newly created habitat on Kasatochi or to an alternate colony on a nearby island.
Polyphenols and Flavonoids in Colombian Fruit and Vegetables - Applications and Benefits: A Review

Fruits and vegetables are important sources of nutritional and therapeutic compounds. Polyphenols and flavonoids are plant secondary metabolites with several biological functions and multiple benefits for humans. Their general chemical characteristics, such as their structures and functional groups, are key to explain their variability and functionality. This review covers 21 Colombian fruits and vegetables containing different amount of polyphenols and flavonoids. They have several applications and offer various benefits, such as antioxidant, bactericidal, and anti-inflammatory activities. Nutritional contributions and therapeutic applications of polyphenols and flavonoids have been reported in multiple studies, and these phytochemicals can be incorporated into dietary products. It is feasible that further beneficial effects of these natural compounds may be discovered in fruits and vegetables found in several regions of Colombia.
Phenotypic Detection of Β-Lactam Antibiotics, Methicillin and Inducible Clindamycin Resistance Among Bacterial Isolates in Patients with Otitis Externa

Background: Otitis is a general terminology used for inﬂammation or infection of the ear; Staphylococcus aureus and Pseudomonas spp. are the most common causes of otitis externa. The resistance mechanism against the beta-lactams group is due to the production of β -lactamase enzymes by the bacteria; the enzymes in staphylococci are encoded by erm genes that confer inducible Clindamycin resistance. Objectives: This study aimed at investigating bacterial resistance by evaluating samples collected from Otitis Externa patients admitted to Ayatollah Roohani Hospital of Babol, Iran. Methods: Ear samples were collected from 72 patients with Otitis Externa referred to Ayatollah Roohani hospital during May 2012 to2013. Atﬁrst,theisolatedbacteriawereidentiﬁedusingappropriatediﬀerentialandselectivemedia,andthenweretestedforan-timicrobialsusceptibilitytestingfollowingthediskdiﬀusionmethod. Specialdiagnostictestswerealsoperformedfortheidentiﬁ-cationof ESBL,iAmpC,pAmpC,metallobetalactamaseproducersandinducibleresistancetoclindamycinandmethicillinresistant strains. Data were analyzed by the SPSS 22 statistical software. Results: Among the 65 isolated bacteria, 24 (36.9%) cases were found to be gram negative and 41 (63.1%) were gram positive; pAmpC beta-lactamase producers were found to have the highest frequency in gram negative bacteria. From 36 (87.8%) isolated CoNS, 18 (50%) bacteria were found to be resistant to the methicillin group and 4 (11.1%) cases had inducible resistance to clindamycin; All isolated S. aureus were sensitive to methicillin and clindamycin. Conclusions: Considering that some bacteria are concurrently able to produce diﬀerent types of resistance enzymes, and also the fact that high prevalence rate of resistance belongs to CoNS, it is important and necessary to perform antimicrobial susceptibility testing as per clinical and laboratory standards institute (CLSI) methods in clinical laboratories.
Grassland ecology in China: perspectives and challenges

During the last few decades, there have been an increasing number of studies on grassland ecology in China, involving the classic ecology concepts or theories and the applicable ecological principles of grassland conservation or management. This paper reviews the main progress in the following aspects. (1) Research on grassland species adaptation and resistance, population dynamics and foraging behavior, and biodiversity and community stability. (2) Research on managed grassland ecosystems (grassland grazing ecology) including grazing effects on grassland ecosystem function and foraging behavior by large herbivores. (3) Global climate change and grassland processes and functioning. (4) Applied research on grassland restoration and ecosystem health assessments such as vegetation restoration, restoration of ecosystem functioning, and assessment methods. There have been significant advances in grassland ecology, including the functions of ecosystem biodiversity, the ecological stoichiometry mechanisms affecting grassland community stability, grazing regulation of plant diversity and nutrient cycling. Grassland ecologists have succeeded in making these advances through observational, experimental and theoretical studies. Nevertheless, there are still significant challenges for the grassland ecology research, including understanding of grassland spatial processes, grassland grazing and multi-functionality, integrated effects of global climate change across grassland areas, as well as the ecological methodology and experimental techniques in grassland ecology.