Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical and Molecular Assessment of Patients with Lynch Syndrome and Sarcomas Underpinning the Association with MSH2 Germline Pathogenic Variants

Lynch syndrome (LS) is a hereditary cancer-predisposing syndrome associated most frequently with epithelial tumors, particularly colorectal (CRC) and endometrial carcinomas (EC). The aim of this study was to investigate the relationship between sarcomas and LS by performing clinical and molecular characterization of patients presenting co-occurrence of sarcomas and tumors from the LS spectrum. We identified 27 patients diagnosed with CRC, EC, and other LS-associated tumors who had sarcomas in the same individuals or families. Germline genetic testing, mismatch repair (MMR) protein immunohistochemistry, microsatellite instability (MSI), and other molecular analyses were performed. Five LS patients presenting personal or family history of sarcomas were identified (3 MSH2 carriers and 2 MLH1), with 2 having Muir–Torre phenotypes. For two MSH2 carriers we confirmed the etiology of the sarcomas (one liposarcoma and two osteosarcomas) as LS-related, since the tumors were MSH2/MSH6-deficient, MSI-high, or presented a truncated MSH2 transcript. Additionally, we reviewed 43 previous reports of sarcomas in patients with LS, which revealed a high frequency (58%) of MSH2 alterations. In summary, sarcomas represent a rare clinical manifestation in patients with LS, especially in MSH2 carriers, and the analysis of tumor biological characteristics can be useful for definition of tumor etiology and novel therapeutic options.
Population structure of Spodoptera frugiperda maize and rice host forms in South America: are they host strains?

Determining which factors contribute to the formation and maintenance of genetic divergence to evaluate their relative importance as a cause of biological differentiation is among the major challenges in evolutionary biology. In Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) two host strains have been recognized in the 1980s: the corn‐strain prefers maize, sorghum, and cotton, whereas the rice‐strain prefers rice and wild grasses. However, it is not clear to what extent these so‐called ‘strains’, which have also been called ‘host races’ or even ‘sibling species’, are really associated with host plants. Due to the indeterminate evolutionary status, we will use the term ‘host forms’ (sensu Funk). Here, we characterized populations collected from maize, rice, and wild grasses from three countries in South America. Using two mitochondrial cytochrome oxidase I (mtCOI) markers and 10 polymorphisms in the triose phosphate isomerase (Tpi) gene, we found various patterns of host association. Two hundred twenty‐seven nuclear amplified fragment length polymorphisms (AFLPs) markers revealed significant genetic differentiation among populations, which was generally correlated to the host from which the larvae were collected. Using a multivariate discriminant analysis and a Bayesian clustering approach, we found that individuals could be grouped into 2–5 genetically distinct clusters, depending on the method. Together, our results indicate that although host‐associated differentiation is present in this species, it does not account for all observable genetic variation and other factors must be maintaining genetic differentiation between these forms. Therefore, the term ‘host strains’ should be abandoned and ‘host forms’ should be used instead for S. frugiperda.
New developments in understanding plant water transport under drought stress.

The Fourth Xylem International Meeting (XIM4) brought together over 100 plant scientists to discuss a wide range of topics related to embolism resistance and efﬁciency of long-distance water transport through plants, and their implications for cultivated and natural systems. The diversity of methods, plant species, and physiological processes discussed in the context of water stress at the meeting highlighted a need to integrate spatial and temporal data about plant functioning, speciﬁcally in regard to climate-change-related challenges.
How Does It Feel to Be Like a Rolling Stone? Ten Questions About Dispersal Evolution

This review proposes ten tentative answers to frequently asked questions about dispersal evolution. I examine methodological issues, model assumptions and predictions, and their relation to empirical data. Study of dispersal evolution points to the many ecological and genetic feedbacks affecting the evolution of this complex trait, which has contributed to our better understanding of life-history evolution in spatially structured populations. Several lines of research are suggested to ameliorate the exchanges between theoretical and empirical studies of dispersal evolution.
Position and cell type‐dependent microtubule reorientation characterizes the early response of the Arabidopsis root epidermis to ethylene

The involvement of cortical microtubules in the control of plant cell expansion was studied in the Arabidopsis root epidermis. In the zone of fast elongation microtubules were transverse to the root axis in all epidermal cells. However when cells entered the differentiation zone cell type-specific microtubule reorientation took place. In the trichoblasts that were then approximately 130 mum long and formed the root hair bulge, the microtubules switched to a random distribution. In the adjoining atrichoblasts microtubules adopted a slightly oblique orientation. In more proximal parts of the differentiation zone atrichoblast microtubules were found in a more oblique and finally in a longitudinal orientation. Upon exposure to ethylene or 1-aminocyclopropane-1-carboxylic acid (ACC - the precursor of ethylene) at a saturating dose, cell elongation abruptly stopped. From then on trichoblast cells reached only a length of about 35 mum, and developed root hairs. Cortical microtubules changed orientation within 10 min. In trichoblasts they adopted the typical random orientation, in atrichoblasts however, they took up a longitudinal orientation. Microtubule reorientation was complete within 60 min. The possible role of microtubules in the control of cell elongation is discussed.
Nanoconfinement of Molecular Magnesium Borohydride Captured in a Bipyridine-Functionalized Metal-Organic Framework.

The lower limit of metal hydride nanoconfinement is demonstrated through the coordination of a molecular hydride species to binding sites inside the pores of a metal-organic framework (MOF). Magnesium borohydride, which has a high hydrogen capacity, is incorporated into the pores of UiO-67bpy (Zr6O4(OH)4(bpydc)6 with bpydc2- = 2,2'-bipyridine-5,5'-dicarboxylate) by solvent impregnation. The MOF retained its long-range order, and transmission electron microscopy and elemental mapping confirmed the retention of the crystal morphology and revealed a homogeneous distribution of the hydride within the MOF host. Notably, the B, N and Mg-edge XAS data confirm the coordination of Mg(II) to the N atoms of the chelating bipyridine groups. In situ 11B MAS-NMR studies helped elucidate the reaction mechanism and revealed that complete hydrogen release from Mg(BH4)2 occurs as low as 200 °C. Sieverts and thermogravimetric measurements indicate an increase in the rate of hydrogen release, with the onset of hydrogen desorption as low as 120 °C, which is approximately 150 °C lower than that of the bulk material. Furthermore, density functional theory calculations support the improved dehydrogenation properties and confirm the drastically lower activation energy for B-H bond dissociation.
Similarities and differences in the peering‐jump behavior of three grasshopper species (Orthoptera: Caelifera)

The peering‐jump behavior was studied for the common field grasshopper Chorthippus brunneus, the meadow grasshopper C. parallelus and the alpine grasshopper Miramella alpina (Orthoptera, Caelifera). It was found that immediately before jumping M. alpina executes primarily unilateral object‐related peering movements, with approximately twice the amplitude and velocity of the predominantly bilateral object‐related peering movements of the other two species. Whereas M. alpina almost always jumped toward the black stripes in the experimental arena, the other species jumped toward both the black stripes and the white spaces between them. All three species preferred the same pattern of black stripes, which permitted them to view one black stripe frontally, with an additional black stripe to the left and right, in the lateral visual field. The similarities and differences in the peering‐jump behavior of the three grasshopper species is discussed with regard to visual perception (parallax cues) and environmental adaptation.
Validation and Refinement of Salmonella pullorum (SP) Colored Antigen for Diagnosis of Salmonella Infections in the Field

3 Abstract: Salmonella infections are major problems for the poultry farming in Bangladesh. The cultural method to identify avian Salmonella infections is laborious and expensive, thus a rapid, sensitive and cost- effective method for the diagnosis of salmonellosis is anticipated. In the present investigation Salmonella pullorum organisms was obtained from the Department of Pathology and it was characterized by culture, biochemical tests and PCR. A neotetrazolium stained Salmonella pullorum antigen was prepared from local isolate of Salmonella pullorum. The protein concentration of stained antigen was measured by BSA standard curve. Prepared antigen was diluted in 2 fold dilution and minimum 72.5 µg/µl antigen concentration showed the positive reaction. Different preservatives (0.5% phenolized saline, 0.5% formalized saline and 0.09% sodium azide) were used to maintain the shelf life of prepared antigen. All the preservatives showed the similar results up to six months. Slide agglutination tests were carried out with un-diluted and diluted anti- sera having known ELISA titre and end point agglutination titre was determined. Serum titre 13942-21362 gave positive result to 2 fold dilution of serum and serum titre 412-771 showed negative result. Different -5 groups of antigens were developed while antigen group-1 (48 h bacterial culture treated with 24 h in neotetrazolium and 2 h in thiomersal) gave the striking positive result. As Group-1 antigen exhibited highest protein concentration (1240 µg/µl) and gave the best result with positive sera, so it was selected for field trial. The seroprevalence of Salmonella infection was 44.39% in a particular poultry farm. The stained antigen was then stored at 4 C. As all used preservatives revealed similar trend of results, so it may be recommend that o 0.5% phenolized saline as preservative because it is cost effective. In the present study, the slide agglutination test was found easy, sensitive, reliable, cost and time effective and needed very small amount of antigen, sera and as well as accessories. Salmonella pullorum antigen from a local isolate was successfully developed which could be used to screen the Salmonella infection in the poultry flocks at the farm premises. It may also be used to determine the antibody titer of the vaccinated flocks.
Germination of seeds of tropical pioneer species under controlled and natural conditions

Seed germination of eight tropical pioneer species (Cecropia hololeuca, C. pachystachya, C. glazioui, Solanum gracillimum, S. granuloso-leprosum, S. tabacifolium, Croton floribundus and Miconia chamissois) was studied. In controlled conditions, alternating temperatures were tested from 5 to 25 °C. Low Red:Far Red ratios (R:FR) were also examined. In the field, germination was evaluated in gaps and under the canopy. With the exception of Croton floribundus, all other species were photoblastic in that higher germination percentages were found under light conditions (S. tabacifolium behaved as a negative photoblastic species at some temperatures). No relationship was found between germination percentage and alternating temperature. Germination was markedly reduced under low R:FR ratios. Alternating temperature is not the main factor affecting field germination. The low R:FR ratio under the canopy seems to be the crucial factor affecting germination.
Chromosome numbers of neotropical Malpighiaceae

For some years I have been accumulating meiotic chromosome counts for neotropical Malpighiaceae, as time and materials made that possible. Some of those counts have been reported by me and my associates in scattered revisionary publications, the rest have never been published, and a number of those are the first counts in their genus. My purpose here is to report all those numbers in one place, and to comment on the systematic implications of some of them. This paper does not pretend to l ist all the chromosome numbers that have been published for neotropical Malpighiaceae, principally because I have not had the opportunity to verify the identity of the vouchers for most of those counts; some of those vouchers probably do not exist. However, I have included in Table 1 a few counts made and published by others but vouchered by specimens whose identif ication I have verif ied, plus one count whose voucher, although currently unavailable for verif ication, I am reasonably confident was identif ied correctly. All of the counts made at the University of Michigan are from pollen mother cells undergoing meiosis; the pairs of chromosomes were stained in the usual acidic preparation with carmine or orcein and counted in squashed cells. Except where a publication is cited in a footnote, all these counts were made by me or Bronwen Gates, who did a number of chromosome counts, especially in the genus Banisteriopsis, when she was working in Malpighiaceae under my direction. All of the vouchers cited are deposited in the University of Michigan Herbarium (MICH) except where some other herbarium is cited. Where two or more vouchers are cited, that species was counted independently in material from each voucher. Except for cases where the voucher is followed by an asterisk (*), all of the counts made at the University of Michigan are documented by permanent microscope slides in my personal collection, which wil l afford the possibil i ty of re-study and correction in the case of counts that might come into question. A star (*) denotes a collection for which I made the count in buds from greenhouse-grown plants derived from the voucher; all other counts made at Michigan were from buds collected from the orisinal voucher.
SOX9 Is Essential for Triple-Negative Breast Cancer Cell Survival and Metastasis

Triple-negative breast cancer (TNBC) has the worst prognosis of all breast cancers, and lacks effective targeted treatment strategies. Previously, we identified 33 transcription factors highly expressed in TNBC. Here, we focused on six sex determining region Y-related HMG-box (SOX) transcription factors (SOX4, 6, 8, 9, 10, and 11) highly expressed in TNBCs. Our siRNA screening assay demonstrated that SOX9 knockdown suppressed TNBC cell growth and invasion in vitro. Thus, we hypothesized that SOX9 is an important regulator of breast cancer survival and metastasis, and demonstrated that knockout of SOX9 reduced breast tumor growth and lung metastasis in vivo. In addition, we found that loss of SOX9 induced profound apoptosis, with only a slight impairment of G1 to S progression within the cell cycle, and that SOX9 directly regulates genes controlling apoptosis. On the basis of published CHIP-seq data, we demonstrated that SOX9 binds to the promoter of apoptosis-regulating genes (tnfrsf1b, fadd, tnfrsf10a, tnfrsf10b, and ripk1), and represses their expression. SOX9 knockdown upregulates these genes, consistent with the induction of apoptosis. Analysis of available CHIP-seq data showed that SOX9 binds to the promoters of several epithelial–mesenchymal transition (EMT)- and metastasis-regulating genes. Using CHIP assays, we demonstrated that SOX9 directly binds the promoters of genes involved in EMT (vim, cldn1, ctnnb1, and zeb1) and that SOX9 knockdown suppresses the expression of these genes. Implications: Our studies identified the SOX9 protein as a “master regulator” of breast cancer cell survival and metastasis, and provide preclinical rationale to develop SOX9 inhibitors for the treatment of women with metastatic triple-negative breast cancer.
Foraging by Mediterranean Horseshoe Bats (Rhinolophus euryale) in Relation to Prey Distribution and Edge Habitat

Abstract We studied the effect of habitat type and prey availability on the foraging decisions of the Mediterranean horseshoe bat (Rhinolophus euryale), a species specialized for cluttered environments. We modeled seasonal habitat selection using radiotelemetry in relation to prey availability in a heterogeneous landscape, determined seasonal diet and prey selection, and used geographic information system data to characterize the landscape surrounding 10 breeding colonies in order to assess the radiotracking results at the population level. Although R. euryale typically has been associated with woodland, our results suggest that the existence of edge habitat, created by semicluttered structures such as hedgerows and woodland edges, was a significant factor in the choice of foraging areas by these bats. Edge habitat was associated with meadows and pastures, creating a landscape highly suited to moths, the preferred prey of R. euryale. In the study area, however, moths were evenly distributed among habitat types; therefore, distribution of moths cannot explain the preference of these bats for semicluttered habitats. The results of our study are consistent with the presumed origin of R. euryale in an edge-rich ecosystem (i.e., the savannahs of northern Africa) and establish a new paradigm for how this species uses habitat. This new paradigm, which might also apply to other members of the genus in Europe, should prompt reconsideration of the presumed habitat requirements for this species, and should be incorporated into the conservation policies for the Mediterranean horseshoe bat.
Polypharmacy, Medication Possession, and Deprescribing of Potentially Non-Beneficial Drugs in Hospice Patients

Patients frequently have comorbidities that when combined with their primary diagnosis qualifies the patient for hospice. Consequently, patients are at risk for polypharmacy due to the number of medications prescribed to treat both the underlying conditions and the related symptoms. Polypharmacy is associated with negative consequences, including increased risk for adverse drug events, drug–drug and drug–disease interactions, reduced functional status and falls, multiple geriatric syndromes, medication nonadherence, and increased mortality. Polypharmacy also increases the complexity of medication management for caregivers and contributes to the cost of prescription drugs for hospices and patients. Deprescribing or removing nonbeneficial or ineffective medications can reduce polypharmacy in hospice. We study medication possession ratios and rates of deprescribing of commonly prescribed but potentially nonbeneficial classes of medication using a large hospice pharmacy database. Prevalence of some classes of potentially inappropriate medications is high. We report possession ratios for 10 frequently prescribed classes, and, because death and prescription termination are competing events, we calculate prescription termination rates using Cumulative Incidence Functions. Median duration of antifungal and antiviral medications is brief (5 and 7 days, respectively), while statins and diabetes medications have slow discontinuance rates (median termination durations of 93 and 197 days). Almost all patients with a proton pump inhibitor prescription have the drug for their entire hospice stay. Data from this study identify those drug classes that are commonly deprescribed slowly, suggesting drug classes and diagnoses that hospices may wish to focus on more closely, as they act to limit polypharmacy and reduce prescription costs.
Status of Biofilm-Forming Genes among Jordanian Nasal Carriers of Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus

Introduction: Biofilm formation in Staphylococcus aureus is a major virulence factor. Both MSSA and MRSA are common causes of community- and hospital-acquired infections and are associated with biofilm formation. The status of biofilm-forming genes has not been explored in Jordanian nasal carriers of S. aureus. This study investigates antibiotic resistance patterns and the prevalence of biofilm-forming genes between MSSA and MRSA in two distinct populations in Jordan. Methods: A total of 35 MSSA and 22 MRSA isolates were recovered from hospitalized patients and medical students at Prince Hamzah Hospital, Jordan. Antibiotic susceptibility was tested using disk diffusion method and Vitek 2 system. The phenotypic biofilm formation was tested using CRA and microtiter plate assays. The prevalence of the biofilm-forming genes was determined using multiplex PCR. Results: Among 57 S. aureus isolates, 22 (38.6%) isolates were MRSA and were highly resistant against benzylpenicillin, oxacillin, and imipenem. The frequencies of the icaADBC were 77.1%, 97.1%, 94.3%, and 97.1% respectively in MSSA compared to 86.4%, 100%, 100%, and 100% in MRSA isolates. On the other hand, the frequency of the fnbA, fnbB, clfA, fib, clfB, ebps, eno, and cna genes was 81.8%, 90.9%, 95.5%, 90.9%, 86.4%, 100%, 100%, and 40.9%, respectively in the MRSA isolates. Conclusion: In both groups, MRSA isolates, in comparison to MSSA, were significantly more resistant to cefoxitin, oxacillin, imipenem, tetracycline, clindamycin, and trimethoprim-sulfamethoxazole. Unexpectedly, biofilm formation and gene prevalence between MRSA and MSSA isolates showed no significant difference, suggesting other potential virulence mechanisms.