Miracle-dz/UniFAR-FTUs huggingface dataset:
GENOTYPIC AND PHENOTYPIC CORRELATION AMONG YIELD COMPONENTS IN BREAD WHEAT UNDER NORMAL AND LATE PLANTINGS

Knowledge of genetic and phenotypic association among economic traits helps plant breeders in outlying efficient breeding strategies for development of high yielding wheat cultivars. Two diverse wheat cultivars forming two contrasting groups viz. tall stature with late maturity (cultivar “Fakhre Sarhad”) vs short stature with early maturity (cultivar “Saleem-2000”) were used to develop the F1, F2 and first backcross generations (BC11 and BC12) from their direct and reciprocal crosses during crop seasons of 200506 and 2006-07 at Cereal Crops Research Institute (CCRI), Pirsabak, Nowshera (Pakistan). Significant genetic variation existed among the six generations for various spike and yield related traits of the direct as well as reciprocal crosses both under normal and late planting environments. Significant and positive genetic correlations among yield related traits predominated the phenotypic association for the direct cross Fakhre Sarhad × Saleem-2000 and its reciprocal under both planting conditions. The strong relationship of yield with yield component traits suggested that grain yield potential can be effectively improved by obtaining maximum expression of spike length, spikes plant -1 , number of grains spike -1 , biological yield and harvest
Optimization and development of regeneration and transformation protocol in Indian mustard using lectin gene from chickpea (Cicer arietinum (L.))

A simple and easy protocol for regeneration and genetic transformation of Brassica juncea (L.) Czern and Coss cv. Pusa bold has been developed. The optimum regeneration was found on combination of BAP (3.0 mg/l) and IAA (0.2 mg/l). The genetic transformation protocol has been standardized using Agrobacterium tumefaciens (gv3101). Cotyledonary petioles used as explant were pre-cultured for 48 h and than co-cultivated with Agrobacterium suspension for 2 days. Putative transformants were selected from selection medium containing 20 mg/l Kanamycine and 250 mg/l cefotaxime. Complete plant formed after placing shoots on rooting medium (0.5 mg/l IBA). Confirmation of integration of transgene was done by PCR using nptII gene primer
Different glycolipids in sperm from different freshwater fishes - A high performance thin-layer chromatography/electrospray ionization-mass spectrometry study.

RATIONALE Glycolipids play important roles in many physiological processes - despite their commonly low abundance. This study summarizes selected data on the (glyco)lipid composition of sperm from different fish species. METHODS Lipid extraction of fish sperm was performed according to the procedure by Bligh and Dyer. The lipid composition of the organic extracts was analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) and electrospray ionization-ion trap (ESI-IT) MS coupled to high performance thin-layer chromatography (HPTLC). RESULTS It was shown that sperm from carp, northern pike, rainbow trout and burbot contain high amounts of neutral and acidic glycosphingolipids as well as sulfoglycolipids. These particular lipids are presumably involved in reproduction requirements. CONCLUSIONS Phospholipids and glycolipids in crude lipid extracts can be analyzed in parallel by MS coupled to TLC. The direct application of tandem MS helps to elucidate the glycolipid structure. Thus, compositional analysis can be performed very rapidly.
Relação entre a lagarta-do-cartucho e seus agentes de controle biológico natural na produção de milho

This work had the objective of quantifying the losses in the maize hybrid BRS 3123 due to the attack of fall armyworm (Spodoptera frugiperda), in the absence or presence of its natural enemies. Fifteen days after the plant emergency, an artificial infestation (one egg mass per square meter) was accomplished. The larvae fed on the plant, without the interference of its natural enemies, by using an appropriated protection cage (initial protection for two days after infestation, until a maximum protection period of 16 days). The damage caused by the pest, determined through a visual scale from 0 (plants without damage) to 5 (dead plants), was on average, 4.01, 1.39, 1.09 and 0.93 for the pest protection period of 16, 6, 4 and 2 days, respectively. In the absence of the biological control agents, the attack of the pest caused losses of 47.27% in the dry matter production and losses of 54.49% in grain yield. The results evidenced the importance of natural enemies in the suppression of fall armyworm in maize crop.
Neuropsychological tests are useful for predicting comorbidities of idiopathic normal pressure hydrocephalus

Comorbidities of idiopathic normal pressure hydrocephalus (iNPH), such as Alzheimer's disease (AD) and Parkinson's spectrum (PS) disorder, can affect the long‐term prognosis of cerebrospinal fluid (CSF) shunting. Therefore, it is important to be able to predict comorbidities in the early stage of the disease. This study aimed to predict the comorbidities of iNPH using neuropsychological tests and cognitive performance evaluation.
Hypoxia and nitrogen processing in the Baltic Sea water column

Steep redoxclines form between oxic surface water and the stagnant, sulfidic hypolimnion in the eutrophied, brackish water Baltic Sea. Nitrification, denitrification, and anammox were measured at and below the redoxcline to quantify the role of water‐column nitrogen processes in the overall magnitude of nitrogen removal in the Baltic Sea. Rates of nitrification were very high (up to 85 nmol N L−1 d−1) at the oxic‐anoxic interface, but, surprisingly, nitrification was separated from the processes reducing nitrate to N2 (up to 810 nmol N L−1 d−1) by tens of meters in depth. N2 production was dominated by chemolithotrophic denitrification, with anammox playing only a negligible role, and limited to the water layers in which nitrite or nitrate coexisted with sulfide. The alternating oxygen concentrations in the basin induce irregular bursts of nitrogen removal. Nitrification takes place after mixing of ammonium‐rich deep water with oxic water, and denitrification uses the formed nitrite and nitrate once anoxic conditions re‐establish. Although removal rates can be high, conditions allowing such rates are likely short‐lived. While the sedimentary denitrification rates at the shallower, oxic areas are lower, they are more constant in time, highlighting the need to avoid hypoxia, which would prevent sedimentary denitrification.
Transient effects of multi‐infusion ketamine augmentation on treatment‐resistant depressive symptoms in patients with treatment‐resistant bipolar depression – An open‐label three‐week pilot study

While the psychiatric benefits of ketamine have been verified through clinical trials, there is limited information about ketamine augmentation in patients with treatment‐resistant bipolar depression (TRBPD). Hence, in the present study, we investigate the therapeutic efficacy and functional brain alterations associated with multi‐infusion ketamine augmentation in patients with TRBPD.
Stock Assessment of the Blue Swimmer Crab Portunus pelagicus (Linnaeus, 1766) from the Oman Coastal Waters

The stock assessment of the blue swimmer crab, Portunus pelagicus was made based on monthly length frequency data collected from four landing sites along the Oman coasts on both Arabian and Oman Seas from January, 2011 to May, 2012. Age and growth have been estimated from the length-frequency distribution of up to 1000 specimens. Age composition was determined using Bhattacharya's method and the results showed that the maximum life span of P. pelagicus was about 15 months. Bertalanffy (1938) growth parameters didn't differ significantly between sexes and the obtained values of K were K = 1.85, 1.68 and 1.68 y -1 and CL values were 102.83, 109.57 and 108.46 mm for male, female and sexes combined, respectively. The values of total mortality coefficient (Z), natural mortality coefficient (M) and fishing mortality coefficient (F) were 7.85, 3.15 and 4.7 y -1 . The yield per recruit and SSB analysis showed that the crab stock is being exploited beyond its maximum biological limit, but the increasing of fishing mortality to the level which gives the maximum Y/R (83% of its current value) will accompanied with a negligible increase in Y/R (2.7%) and a considerable decrease in both biomass per recruit (21.1%) and spawning stock biomass (37.6%).
Latent Tuberculosis Infection Increases in Kidney Transplantation Recipients Compared With Transplantation Candidates: A Neglected Perspective in Tuberculosis Control

Abstract Background The prevalence and incidence of latent tuberculosis infection (LTBI) in patients with kidney transplantation remain unclear. Methods In this prospective study, we enrolled kidney transplantation candidates (KTCs) and recipients (KTRs) from 2014 to 2018. We defined LTBI as a positive result of QuantiFERON-TB Gold In-tube (QFT). We analyzed the predictors for LTBI acquisition and followed up on QFT assay test for 2 years among those initially without LTBI. Results Of 425 patients enrolled, 305 (71.8%) patients belonged to the KTC group and 120 (28.2%) to the KTR group. The initial QFT showed positive results in 32 (10.5%) and 24 (20.0%) patients in the KTC and KTR groups, respectively (P = .009). The QFT response value in patients with LTBI was higher in the KTR group than in the KTC group (1.85 vs 1.06 IU/mL, P = .046). Multivariate logistic regression showed that old age, absence of bacillus Calmette–Guérin (BCG) scar, presence of donor-specific antibody, and KTR group were independent factors for positive LTBI. For participants with initial negative QFT, positive QFT conversion within a 2-year follow-up was higher after kidney transplantation (20%) than in KTCs (5.5%) (P = .034). Conclusions This study is the first cohort to follow up LTBI status in patients with kidney transplantation and shows its higher prevalence and incidence in KTRs. It indicates that surveillance of LTBI after renal transplantation is important. In addition to status of kidney transplantation, old age, no BCG vaccination, and positive donor-specific antibody are also positive predictors for LTBI.
CommonRoad Drivability Checker: Simplifying the Development and Validation of Motion Planning Algorithms

Collision avoidance, kinematic feasibility, and road-compliance must be validated to ensure the drivability of planned motions for autonomous vehicles. Although these tasks are highly repetitive, computationally efficient toolboxes are still unavailable. The CommonRoad Drivability Checker—an open-source toolbox—unifies these mentioned checks. It is compatible with the CommonRoad benchmark suite, which additionally facilitates the development of motion planners. Our toolbox drastically reduces the effort of developing and validating motion planning algorithms. Numerical experiments show that our toolbox is real-time capable and can be used in real test vehicles.
HIGH THROUGHPUT SCREENING OF PRIMING CANDIDATES FOR IMPACT ON NONVIRAL GENE DELIVERY

Priming, in the context of nonviral gene delivery, is the treatment of cells with a compound prior to gene transfer that enhances transfection efficiency and/or transgene expression. Essentially, it is the application of an adjuvant approach to gene delivery. Effective transfection strategies may require priming to compete with the efficiency of viral transduction in order to achieve clinically relevant efficiency and expression in vivo. To search for priming compounds, a high throughput screen of the NIH Clinical Collection was performed using 25kDa b-PEI, an EGFP/luciferase plasmid, and HEK293T cells. The EGFP reporter was multiplexed with Hoechst 33342 and Resazurin fluorescence to measure transfection efficiency, transgene expression, proliferation, and viability of the cells in response to priming with the screened NCC compounds and PEI transfection. The screen identified dozens of compounds and several compound classes that appear to affect transfection through modulation of mitochondrial dysfunction in response to the toxicity of PEI complexes. With further investigation and development, the mechanisms by which these and other priming compounds are affecting gene transfer can be understood and applied towards the development of efficient gene delivery strategies. iii ACKNOWLEDGEMENTS There are many people to whom I owe a debt of gratitude for their role in the work and in my life while I completed this thesis research: Jared Beyersdorf, formerly an undergraduate in the Pannier Lab, performed a preliminary screen for transfection priming compounds, the protocols from which the screening methods in thesis research were developed. He's also a cool guy who is on to bigger and better things. My fellow graduate students and staff in the BSE department at UNL, especially the Pannier Lab members (who were most often helpful, and happy diversions otherwise. Drs. Mark Riley and Nicole Iverson for their comments and guidance, and patience, as committee members for my thesis and defense. Dr. Deepak Keshwani for graciously allowing me to use his fluorescence plate reader. Also, Danielle Shea, for helping me with flow cytometry that doesn't appear in this work. I'm most extremely grateful to my advisor, Dr. Angela Pannier, for having faith in me, and giving me a chance to complete this Master's thesis research. I've learned a lot from working with you, and I hope I continue to live up to your expectations. Finally, thanks to my family for supporting me on my wandering path. I love you so much.
TOX is expressed by exhausted and polyfunctional human effector memory CD8+ T cells

The transcription factor TOX is not exclusively linked to T cell exhaustion (see the related Focus by Utzschneider and Kallies). The TOX profiles of T cells Transcription factors TOX and TCF-1 have emerged as key drivers of exhaustion and stemness programs in CD8+ T cells. Using bulk and single-cell transcriptome analyses and flow cytometric analyses, Sekine et al. have generated a detailed map of TOX and TCF-1 expression in human CD8+ T cells. TOX is generally expressed by effector memory CD8+ T cells and is not restricted to exhausted T cells, whereas TCF-1 demarcates early-differentiated, memory CD8+ T cells. Using tetramers to examine the specificity of antigen-specific CD8+ T cells, they found that cytotoxic memory CD8+ T cells targeting both pathogenic and well-controlled chronic infections are more likely to express TOX. Their results propose that TOX-dependent transcriptional wiring is not restricted to exhausted CD8+ T cells. CD8+ T cell exhaustion is a hallmark of many cancers and chronic infections. In mice, T cell factor 1 (TCF-1) maintains exhausted CD8+ T cell responses, whereas thymocyte selection-associated HMG box (TOX) is required for the epigenetic remodeling and survival of exhausted CD8+ T cells. However, it has remained unclear to what extent these transcription factors play analogous roles in humans. In this study, we mapped the expression of TOX and TCF-1 as a function of differentiation and specificity in the human CD8+ T cell landscape. Here, we demonstrate that circulating TOX+ CD8+ T cells exist in most humans, but that TOX is not exclusively associated with exhaustion. Effector memory CD8+ T cells generally expressed TOX, whereas naive and early-differentiated memory CD8+ T cells generally expressed TCF-1. Cytolytic gene and protein expression signatures were also defined by the expression of TOX. In the context of a relentless immune challenge, exhausted HIV-specific CD8+ T cells commonly expressed TOX, often in clusters with various activation markers and inhibitory receptors, and expressed less TCF-1. However, polyfunctional memory CD8+ T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) also expressed TOX, either with or without TCF-1. A similar phenotype was observed among HIV-specific CD8+ T cells from individuals who maintained exceptional immune control of viral replication. Collectively, these data demonstrate that TOX is expressed by most circulating effector memory CD8+ T cell subsets and not exclusively linked to exhaustion.
Fast whole brain MR imaging of dynamic susceptibility contrast changes in the cerebrospinal fluid (cDSC MRI)

The circulation of cerebrospinal fluid (CSF) is closely associated with many aspects of brain physiology. When gadolinium(Gd)‐based contrast is administered intravenously, pre‐ and post‐contrast MR signal changes can often be observed in the CSF at certain locations within the intra‐cranial space, mainly due to the lack of a blood‐brain barrier in the dural blood vessels. This study aims to develop and systemically optimize MRI sequences that can detect dynamic signal changes in the CSF after Gd administration with a sub‐millimeter spatial resolution, a temporal resolution of <10 s, and whole brain coverage.
Brief Review on Local Chicken Breeds in Korea with Respect to Growth Performance and Meat Quality

Local breeds are known to possess favorable characteristics such as resistance to som e pathogens, superior meat flavor and taste and high dressing percentage. Due to these characteristics, higher consumption of meat product from local chickens has been on increase in countries such as East Asia and Europe and consumers are willing to pay premium price. There are four locally available chicken breeds bred for and consumed as a nutritive and medicine food in Korea. These are White-mini broilers, Hanhyup-3-ho, Woorimatdag and Silky fowl. Due to the increase in consumer preference on healthy foods, demand on meat products from local chicken breeds has been surged. The current review is aimed to briefly introduce the growth and meat characteristics of local chicken breeds in Korea.
The effect of NaCl priming on cucumber seedling growth under salinity stress

Seeds of two Iranian cucumber cultivars, Basmenj and Varamin, were primed (P) with 15 dS m -1 NaCl solution for 36 h at 20°C. Non-primed (NP) and primed (P) seeds were sown in trays containing perlite. The trays were placed in an unheated greenhouse and irrigated with different levels of NaCl solution (0.3 (control), 2.5, 5, 9 and 13 dS m -1 ) for a period of 4 weeks. Total emergence, emergence rate, radicle length and dry weight of seedlings derived from P seeds were higher than NP seeds. NaCl priming increased uptake of K and Ca and accumulation of proline in cucumber seedlings. These results indicated that NaCl priming increased salt tolerance of cucumber seedlings by promoting K and Ca accumulation in addition to inducing osmoregulation by accumulation of proline.
Putative virulence factors of Candida species colonizing respiratory tracts of patients

The objective of this research was to investigate the patterns of Candida species colonizing respiratory tracts of hospitalized patients and their production of putative virulence factors in vitro. One hundred and twenty-nine Candida isolates were collected from respiratory tract specimens of adult Jordanian patients admitted to Jordan University Hospital (JUH) during the period 1999–2001. The patterns of colonization were as follows. C. albicans accounted for (67%) of the isolates, followed by non-C. albicans isolates (33%), including C. krusei (12%), C. tropicalis (11%), C. glabrata (6%) and other Candida spp. (4%). No significant differences were determined between the Candida isolates as regards their secretion in vitro of variable amounts of putative virulence factors – aspartyl proteinase, phospholipase and haemolysin (p>0.05). However, the mean production of proteinase using qualitative measurements is clearly more observed in C. albicans isolates colonizing the respiratory tract. The study concludes that putative virulence factors alone are not responsible for the colonization potential of Candida species.
Scale-dependent and multi-metric nest habitat thresholds for Red-headed Woodpeckers at the northern periphery of their range

ABSTRACT The relation between species occurrence and the structure or composition of habitat can be complex and often varies in a species-specific manner. Sometimes, species–habitat relations are defined by thresholds, or abrupt nonlinear responses to a habitat gradient. Threshold responses are expected when certain habitat features are required for species occurrence. For example, primary cavity-nesting woodpeckers often typify the threshold concept because in the absence of appropriate substrates (decadent wood) large enough for nest cavities, woodpeckers will not occur. In such cases, identifying thresholds is important to ensure that management activities meet minimal (or maximal) habitat requirements of target species. The Red-headed Woodpecker (Melanerpes erythrocephalus) is a species of national conservation concern, and loss of suitable nesting habitat has been suggested as a primary factor in its population declines. Threshold responses may partly explain why this species has gone locally extinct in areas where land-use change resulted in a transition from suitable to unsuitable habitat. Here, we tested whether a regionally important population of Red-headed Woodpeckers in northern New York, near the periphery of the species' range, exhibited threshold responses in their selection of nesting habitat. We used boosted regression trees (BRT) to identify nest habitat thresholds in relation to multiple habitat variables at multiple spatial scales (nest tree, forest patch, and forest stand). We identified nest tree thresholds related to tree decay class (≥33% decadent canopy), cumulative dead limb length (≥4 m), and tree diameter (≥34 cm dbh). Forest patch (vegetation surrounding nest tree; 0.04 ha) thresholds were related to cumulative dead limb length (≥17 m), woody understory height (<12 cm), mean tree diameter (30 cm dbh), and large tree (≥30 cm dbh) density of ≥4. Forest stand thresholds were related to overall stand decadence (on average trees have ≥1% crown decay) and woody understory height (<12 cm). Red-headed Woodpeckers exhibited scale-dependent and multi-metric nest habitat thresholds, which indicate that a lack of suitable nesting habitat (i.e. habitats meeting or exceeding multi-metric and multi-scale criteria) may be limiting population growth near the periphery of the species' range. In particular, the abundance of decadent (dead and decaying) tree resources appears to limit the distribution of suitable habitat. Our objective threshold criteria can be used to identify habitats of high conservation value for this species, or to identify specific habitat features that require management or restoration to increase suitable habitat for this threatened species.