Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Growth Promoting Rhizobacteria Effect on Antioxidant Status, Photosynthesis, Mineral Uptake and Growth of Lettuce under Soil Salinity

This study was carried out to investigate the effects of plant growth promoting rhizobacteria (PGPR) on the antioxidant status, photosynthesis, mineral content and growth of lettuce (Lactuca sativa L.) under different soil salinity conditions. Increasing salinity in the soil decreased plant growth, photosynthesis, stomatal conductance, chlorophyll content, and mineral uptake compared to soil without salinity. Inoculation with two PGPR strains, Serratia sp. and Rhizobium sp. , into saline soils alleviated the salinity effects on the antioxidant enzymes ascorbate peroxidase (APX) and glutathione reductase (GR), along with those on photosynthesis, mineral content and growth. As a result, an increase in salinity in the soil caused a physiological response or disorder in lettuce plants. Treatment with PGPR strains could alleviate the effect of potentially toxic ions.
In vitro Maturation of Rabbit Oocytes as Affected by Donor Age and Type of Serum From Mated Does in Maturation Medium

This study was designed to examine the effect of the age of rabbit and addition of serum at different reproductive status (pre-, at and post-mating doe serum) in maturation medium (TCM-199) as compared as hormonal addition (10 IU eCG and 20 IU hCG/ml) on in vitro maturation of rabbit oocytes. Results show that frequency distribution of oocytes at MII stage was higher (P<0.05) for oocytes recovered from old (59.58%) than young (51.69%) rabbits. Frequency distribution of oocytes at MI stage showed an opposite trend, being significantly (P<0.05) lower for oocytes recovered from old (9.58%) than the small (14.89%). Frequency distribution of oocytes at MII was the highest (62.11%, P<0.05) for oocytes in vitro maturated in maturation medium supplemented with post-mating serum, but did not differ significantly from those in vitro matured in media supplemented with hormones (57.54%) or pre-mating serum (55.87%), while oocytes matured with mating serum showed significantly the lowest values (46.78%). Frequency distribution of oocytes at MI stage showed an opposite trend to that at MII. The interaction between age of oocyte donors and type of serum was not significant on frequency distribution of oocytes at all maturation stages. Such effect was reflected in higher maturation rat (oocyte at MII) for oocytes matured with Post-mating serum for young or old doners, but in vitro maturation rate was the highest (67.5%) for oocytes recovered from older doners and in vitro matured in medium supplemented with post-mating serum. Results of the current study revealed that the highest percentage of oocytes at metaphaseII (matured oocytes) and the lowest percentage of degenerated oocytes were obtained when rabbit oocytes were recovered at older ages and cultured in TCM-199 supplemented with serum from post-mating doe serum or hormones (eCG and hCG).
Correlations between age of Bali bull and semen production at National Artificial Insemination Center, Singosari - Indonesia

The aim of this research was to analyze the correlation of age of Bali bull to the body weight and semen qualities. The materials were 50 Balibulls data collected from 2012 to 2018. Therecordeddatawere consisted ofsemen productions (n = 1304) and body weight (n = 1544). The observation was conducted to analysis the interrelationship between the Bali bulls age and body weight (BW), to the semen volume (SV), individual motility (IM) and sperm concentration (SC). The obtained data was analyzed with One-Way ANOVA analysisby using SPSS 24 and followed with Duncan’s Multiple Range Test to determine any significant differences. The correlation between Bali bulls age (the independent variable) and semen quality (the dependent variable) was computed by using Pearson correlation method and presented in linear regression models. The results showed that the Bali bulls agesignificantly affect (P<0.05) the BW from the age of 1 to 10 years old. The age also showed a significant effect (P<0.05) on the semen qualities. The age correlated significantly (P<0.05) with BW, SV, IM, SC were 0.658, 0.386, 0.134 and 0.086, respectively. Inconclusion,the age of Bali bull could be used as an indicator todetermineits BWand semenqualities.
Replication Gaps Underlie BRCA Deficiency and Therapy Response

This study suggests that ssDNA replication gaps are fundamental to the toxicity of genotoxic agents and underlie the BRCA-cancer phenotype "BRCAness," yielding promising biomarkers, targets, and opportunities to resensitize refractory disease. Defects in DNA repair and the protection of stalled DNA replication forks are thought to underlie the chemosensitivity of tumors deficient in the hereditary breast cancer genes BRCA1 and BRCA2 (BRCA). Challenging this assumption are recent findings that indicate chemotherapies, such as cisplatin used to treat BRCA-deficient tumors, do not initially cause DNA double-strand breaks (DSB). Here, we show that ssDNA replication gaps underlie the hypersensitivity of BRCA-deficient cancer and that defects in homologous recombination (HR) or fork protection (FP) do not. In BRCA-deficient cells, ssDNA gaps developed because replication was not effectively restrained in response to stress. Gap suppression by either restoration of fork restraint or gap filling conferred therapy resistance in tissue culture and BRCA patient tumors. In contrast, restored FP and HR could be uncoupled from therapy resistance when gaps were present. Moreover, DSBs were not detected after therapy when apoptosis was inhibited, supporting a framework in which DSBs are not directly induced by genotoxic agents, but rather are induced from cell death nucleases and are not fundamental to the mechanism of action of genotoxic agents. Together, these data indicate that ssDNA replication gaps underlie the BRCA cancer phenotype, “BRCAness,” and we propose they are fundamental to the mechanism of action of genotoxic chemotherapies. Significance: This study suggests that ssDNA replication gaps are fundamental to the toxicity of genotoxic agents and underlie the BRCA-cancer phenotype “BRCAness,” yielding promising biomarkers, targets, and opportunities to resensitize refractory disease. See related commentary by Canman, p. 1214
Humans adapt their anticipatory eye movements to the volatility of visual motion properties

Animal behavior must constantly adapt to changes, for example when the statistical properties of the environment change unexpectedly. For an agent that interacts with this volatile setting, it is important to react accurately and as quickly as possible. It has already been shown that when a random sequence of motion ramps of a visual target is biased to one direction (e.g. right or left), human observers adapt to accurately anticipate the expected direction with their eye movements. Here, we prove that this ability extends to a volatile environment where the probability bias could change at random switching times. In addition, we also recorded the explicit direction prediction reported by observers as given by a rating scale. Both results were compared to the estimates of a probabilistic agent that is optimal in relation to the event switching generating model. Compared to the classical leaky integrator model, we found a better match between our probabilistic agent and the behavioral responses, both for the anticipatory eye movements and the explicit task. Furthermore, by titrating the level of preference between exploration and exploitation in the model, we were able to fit each individual experimental data-set with different levels of estimated volatility and derive a common marker for the inter-individual variability of participants. These results prove that in such an unstable environment, human observers can still represent an internal belief about the environmental contingencies, and use this representation both for sensory-motor control and for explicit judgments. This work offers an innovative approach to more generically test the diversity of human cognitive abilities in uncertain and dynamic environments. Author summary Understanding how humans adapt to changing environments to make judgments or plan motor responses based on time-varying sensory information is crucial for psychology, neuroscience and artificial intelligence. Current theories for how we deal with the environment’s uncertainty most rely on the equilibrium behavior in response to the introduction of some randomness change. Here we show that in the more ecological case where the context switches at random times all along the experiment, an adaptation to this volatility can be performed online. In particular, we show in two behavioral experiments that humans can adapt to such volatility at the early sensorimotor level, through their anticipatory eye movements, but also at a higher cognitive level, through explicit ratings. Our results suggest that humans (and future artificial systems) can use much richer adaptive strategies than previously assumed.
Mitigating ARP Cache Poisoning Attack in Software-Defined Networking (SDN): A Survey

Address Resolution Protocol (ARP) is a widely used protocol that provides a mapping of Internet Protocol (IP) addresses to Media Access Control (MAC) addresses in local area networks. This protocol suffers from many spoofing attacks because of its stateless nature and lack of authentication. One such spoofing attack is the ARP Cache Poisoning attack, in which attackers poison the cache of hosts on the network by sending spoofed ARP requests and replies. Detection and mitigation of ARP Cache Poisoning attack is important as this attack can be used by attackers to further launch Denial of Service (DoS) and Man-In-The Middle (MITM) attacks. As with traditional networks, an ARP Cache Poisoning attack is also a serious concern in Software Defined Networking (SDN) and consequently, many solutions are proposed in the literature to mitigate this attack. In this paper, a detailed survey on various solutions to mitigate ARP Cache Poisoning attack in SDN is carried out. In this survey, various solutions are classified into three categories: Flow Graph based solutions; Traffic Patterns based solutions; IP-MAC Address Bindings based solutions. All these solutions are critically evaluated in terms of their working principles, advantages and shortcomings. Another important feature of this survey is to compare various solutions with respect to different performance metrics, e.g., attack detection time, ARP response time, calculation of delay at the Controller etc. In addition, future research directions are also presented in this survey that can be explored by other researchers to propose better solutions to mitigate the ARP Cache Poisoning attack in SDN.
Single cell transcriptomics of human epidermis reveals basal stem cell transition states

How stem cells give rise to human interfollicular epidermis is unclear despite the crucial role the epidermis plays in barrier and appendage formation. Here we use single cell-RNA sequencing to interrogate basal stem cell heterogeneity of human interfollicular epidermis and find at least four spatially distinct stem cell populations that decorate the top and bottom of rete ridge architecture and hold transitional positions between the basal and suprabasal epidermal layers. Cell-cell communication modeling through co-variance of cognate ligand-receptor pairs indicate that the basal cell populations distinctly serve as critical signaling hubs that maintain epidermal communication. Combining pseudotime, RNA velocity, and cellular entropy analyses point to a hierarchical differentiation lineage supporting multi-stem cell interfollicular epidermal homeostasis models and suggest the “transitional” basal stem cells are stable states essential for proper stratification. Finally, alterations in differentially expressed “transitional” basal stem cell genes result in severe thinning of human skin equivalents, validating their essential role in epidermal homeostasis and reinforcing the critical nature of basal stem cell heterogeneity.
Influence of Integrated Nutrient Management Practices On Soil Properties and Yield of Potato (Solanum tuberosum. L) in an Inceptisol of Khajura, Banke

Field experiment was conducted at the research farm of Regional Agriculture Research Station (RARS), Khajura to evaluate the influence of integrated nutrient management options that could enhance the properties of soil and yield of potato under the different climatic conditions of Khajura. The experiment was started in November 2016 in randomized complete block design with different seven treatments of nutrients using Farm yard manure (FYM), Poultry manure (PM) Vermicompost (VC). Available N, P and K status in the soil increased gradually due to the application of inorganic and organic fertilizers. The plots receiving 50 % RDNPK through inorganic fertilizers and remaining 50% RDN through PM registered the highest available N, P and K status in the soil. The highest pH (6.3) content in soil was found in plots treatments with poultry manure and inorganic fertilizers. Potato plots treated with FYM and inorganic fertilizers produced higher SOM content in soil after harvest (2.38%) as compared to control plots (2.09%). The treatments integrated with FYM show less bulk density than the control plot. Organic manures treated plots produce taller plants as compared plots receiving inorganic fertilizers only. Integrated use of 50 % recommended dose of NPK through inorganic fertilizers and remaining 50% RDN through PM produced higher numbers of tubers per plot (304 tubers per plot) and total tuber yield (22.86 tha-1). Int. J. Appl. Sci. Biotechnol. Vol 7(3): 365-369
Identifying microbes from environmental water samples

What is the microbe that we are dealing with? Whether it is cholera or anthrax, we want to know the disease-causing microorganism as quickly as possible since prompt identification of the causative organism would help control disease spread and potentially save lives through provision of appropriate care and medication. Yet, despite the advent of rapid microbial identification tools – particularly those based on mass spectrometry – most undergraduate curricula continue to focus on cultureand nucleic acid-based identification techniques since they are widely used for detecting and identifying microbes in clinical and environmental samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories but are rarely featured in undergraduate curricula. Motivated by the desire to address the curriculum gap, the author of this study developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry-based microbial identification. By requiring students to identify microbes in environmental water samples – a real-life problem with unknown answers – the exercise piqued the students’ interest in learning, while helping to stir their curiosity through an interesting field activity in which they could put on a scientist’s hat in solving a mystery. This synopsis article summarizes a piece of published educational research and expands on the discussion of concepts underlying matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification. Herein, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. Additionally, the effect of general and tailored sample preparation protocols on identification accuracy is also elaborated. Finally, the pedagogical utility of fieldand inquiry-based educational tools is also discussed in greater detail from a post-publication perspective. A full-length synopsis of the work and a structured abstract can be found in the accompanying PDF file, the original article being entitled: “Teaching Microbial Identification with World News of Natural Sciences 2 (2015) 7-19 -8Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools”.
Conception and Evaluation of an Interdisciplinary Lecture on Tooth Extraction versus Tooth Preservation

Background: Despite consistent demands, examples of interdisciplinary and evidencebased curricula are rare in dentistry. To address this, the following pilot study describes the conception of an interdisciplinary curriculum on the topic of tooth extraction (TE) vs. tooth preservation (TP). Methods: Based on the German National Learning Objective Catalog on Dentistry, 1408, learning objectives were analyzed, and an interdisciplinary lecture series on TE vs. TP was conceived and conducted. Students’ knowledge increase was measured using self-assessment questionnaires on a 6-step Likert scale (from 1 = very good to 6 = insufficient) and by structured evaluation. Results: Overall, the students rated their theoretical knowledge significantly better (p < 0.001) and the pilot course was evaluated “well” to “very well” by the students in terms of didactics, relevance, extent, and involvement. Discussion: The pilot course allowed students to choose between tooth extraction and tooth preservation based on an evidence-based and interdisciplinary assessment.
A native prokaryotic voltage-dependent calcium channel with a novel selectivity filter sequence

Voltage-dependent Ca2+ channels (Cavs) are indispensable for coupling action potentials with Ca2+ signaling in living organisms. The structure of Cavs is similar to that of voltage-dependent Na+ channels (Navs). It is known that prokaryotic Navs can obtain Ca2+ selectivity by negative charge mutations of the selectivity filter, but native prokaryotic Cavs had not yet been identified. Here, we report the first identification of a native prokaryotic Cav, CavMr, and its relative, NavPp. Although CavMr contains a smaller number of negatively charged residues in the selectivity filter than artificial prokaryotic Cavs, CavMr exhibits high Ca2+ selectivity. In contrast, NavPp, which has similar filter sequence to artificial Cavs, mainly allows Na+ to permeate. Interestingly, a NavPp mutant whose selectivity filter was replaced with that of CavMr exhibits high Ca2+ selectivity. Mutational analyses revealed that the glycine residue of the CavMr selectivity filter is a determinant for Ca2+ selectivity. This glycine residue is well conserved among subdomains I and III of eukaryotic Cavs. These findings provide new insight into the Ca2+ selectivity mechanism conserved from prokaryotes to eukaryotes. Significance Statement CavMr is the first identified native prokaryotic Cav. CavMr has a unique selectivity filter sequence different from that of artificial prokaryotic Cavs derived from canonical prokaryotic Navs. Unlike artificial Cavs, the glycine residue of the selectivity filter of CavMr is important for the selective permeation of Ca2+ ions, indicating that there are two different mechanisms of Ca2+ recognition. Interestingly, corresponding glycine residues are found in subdomains I and III of eukaryotic Cavs. These findings suggest that the small glycine residue in the Cav selectivity filter is an overlooked feature determining Ca2+ selectivity. Therefore, further investigation of CavMr will contribute to our understanding of the principles underlying Ca2+ selectivity.
Identification and quantification of phthalates in water and sediment of Ori Stream, Iwo, Southwestern Nigeria using high performance liquid chromatography

This study provides data on distribution of phthalate esters (PAEs) in the water and sediments in the Ori stream, Iwo, Nigeria. The liquid-liquid extraction method was employed, followed by cleaned up in an alumina column using hexane. Chromatographic separation and quantification were done using Zorbax Eclipse AAA C18 analytical column. The concentrations of DMP, DBP, DEP, and DPP in water (µg/L) ranged from 1.29±1.3 in DBP to 938±780 in DMP while in sediment (µg/kg) ranged from 12.7±15 in DEP to 152±140 µg/kg in DBP. These concentrations were above the USEPA limits of 3 µg/L as recommended for phthalates in water. Key words: Phthalates, liquid-liquid extraction, high performance liquid chromatography (HPLC), endocrine disruptors, stream.
Effects of DCM Leaf Extract of Gnidia glauca (Fresen) on Locomotor Activity, Anxiety, and Exploration-Like Behaviors in High-Fat Diet-Induced Obese Rats

Obesity is the main component of metabolic syndromes involving distinct etiologies which target different underlying behavioral and physiological functions within the brain structures and neuronal circuits. An alteration in the neuronal circuitry stemming from abdominal or central obesity stimulates a cascade of changes in neurochemical signaling that directly or indirectly mediate spontaneously emitted behaviors such as locomotor activity patterns, anxiety and exploration. Pharmacological agents available for the treatment of neurologic disorders have been associated with limited potency and intolerable adverse effects. These have necessitated the upsurge in utilization of herbal prescriptions due to their affordability, easy accessibility and are firmly embedded within wider belief systems of many people. Gnidia glauca has been used in management of many ailments including obesity and associated symptomatic complications. However, its upsurge in use has not been accompanied with authentication of these folkloric claims. The present study aimed to determine the modulatory effect of Dichloromethane leaf extract of Gnidia glauca on locomotor activity, exploration and anxiety-like behaviors in high fat diet-induced obese rats in an Open Field Arena. Obesity was experimentally induced by feeding the rats with prepared high fat diet and water ad libitum for a period of 6 weeks. The in-vivo anti-obesity effects were determined by oral administration of G. glauca at dosage levels of 200, 250 and 300mg/kg body weight in high fat diet-induced obese rats from the 6th to 12th week. Phytochemical analysis was done using gas chromatography linked to mass spectroscopy. Results indicated that Gnidia glauca showed anxiolytic effects and significantly increased spontaneous locomotor activity and exploration-like behaviors in HFD-induced obese rats. The plant extract also contained phytocompounds that have been associated with amelioration of the main neurodegenerative mediators viz inflammation and oxidative stress. These findings provide ‘qualified leads’ for the synthesis of new alternative therapeutic agent for management of neurologic disorders. However, there’s need to conduct toxicity studies of Gnidia glauca to establish its safety profiles.
Exploring Fault-Tolerant Erasure Codes for Scalable All-Flash Array Clusters

Large-scale systems with all-flash arrays have become increasingly common in many computing segments. To make such systems resilient, we can adopt erasure coding such as Reed-Solomon (RS) code as an alternative to replication because erasure coding incurs a significantly lower storage overhead than replication. To understand the impact of using erasure coding on the system performance and other system aspects such as CPU utilization and network traffic, we build a storage cluster that consists of approximately 100 processor cores with more than 50 high-performance solid-state drives (SSDs), and evaluate the cluster with a popular open-source distributed parallel file system, called Ceph. Specifically, we analyze the behaviors of a system adopting erasure coding from the following five viewpoints, and compare with those of another system using replication: (1) storage system I/O performance; (2) computing and software overheads; (3) I/O amplification; (4) network traffic among storage nodes, and (5) impact of physical data layout on performance of RS-coded SSD arrays. For all these analyses, we examine two representative RS configurations, used by Google file systems, and compare them with triple replication employed by a typical parallel file system as a default fault tolerance mechanism. Lastly, we collect 96 block-level traces from the cluster and release them to the public domain for the use of other researchers.